It sort of depends on what you call "civilization". Do you mean something on the scale of Ancient Egypt? Then the answer is that it's highly unlikely. If you mean something smaller, then the possibility goes up depending on how arbitrarily small you are willing to consider.

The Holocene Wet Phase begins around 10,500 years ago. Prior to that, the Sahara was desert, slightly drier and bigger than it is today. Between 10,500 years and 9,000 years ago, the Sahara became wetter, and gradually grasslands with patches of forested areas appeared. This wet period lasted until about 7,300 years ago, when it started getting drier again. The drying was quite slow initially, but accelerated dramatically about 4,000 years ago when it became very dry very quickly (over a period of about 100 years).

Typically, "civilization" requires an economy to support it. The hunter-gatherer lifestyle is not conducive to a growing economy, though there have been exceptions such as Gobekli Tepe, where hunter-gatherers have left archeological remains of complex group activity such as monumental architecture. But this happens in very rare areas that are exceptionally rich in resources. The Sahara, even in its wet phase, was never that rich. Nor have we found any monumental remains there predating Ancient Egypt.

So it seems that the odds of finding a "civilization" would be low prior to agriculture, or at least pastoralism. Both were introduced to the region around 7,000 years ago, which kind of sets a cut-off date for the earliest civilizations.

If you look at maps of archeological sites in Egypt, you can kind of see how the population was distributed. This map shows archeological sites by date. At 10,500 years it's all desert, the wet phase has barely begin, population is still clustered around the Nile. Between 10,500 and 7.300 years ago (the duration of the wet phase), population spreads out. Many sites are known as you can see by the red dots on the map. None show signs of "civilization" - they are mostly small settlements with hearths, small shelters, few artifacts. Note that almost all of them are in what is desert today, so it's not like people have a very hard time finding sites in the desert.

After 7,300 years ago (when agriculture and pastoralism arrived), the population retreats back to the Nile, except for a few isolated desert oases. As you can see on the map, they are very scarce. This would be the best period for your question about unknown civilizations, since it's after the arrival of agriculture and pastoralism, but before the beginnings of Ancient Egypt. The Nile area has been very well excavated, and it seems unlikely that any huge discoveries about prior civilizations remain. It's possible that there are ancient oases in the desert which have since dried up and disappeared under the sands, but these would probably not support any large civilizations. So what you are really looking for is remains of cultures that were somewhat ahead of their times in population, organization and technology, but still restricted to desert oases.

This figure shows the archeology of known sites in Egypt. The greenish background represents the wet phase, brown represents desertification. The y-axis is latitude and the x-axis is time, so you can see the desert encroaching from the north as the Sahara dries up. If you open up Google Maps or an atlas to follow along and locate the areas, you can see that the highest density of early settlements is actually in the Great Sand Sea, which is the western border of Egypt/Libya today, and deep desert. It has preserved artifacts exceptionally well, but they only show primitive settlements, no advanced civilizations. As population density increases, people spread out to the Selima Sand Sheet at the southwest corner of Egypt, another area of sand dunes and extreme desert. These regions support pastoralism, but not agriculture, which is another point against advanced civilizations in the desert.

Well, to answer your question...Yes! Where else would it be? The entirety of the Holocene environment, artifacts, and burials are all covered by the desert. If you analyze long wave length radar images taken by the space shuttle you'll see that the Sahara is in fact covering the obvious trails left by rivers and megalakes during the Holocene: A blogpost by NASA on the subject, and The Sahara Megalakes Project by King's College London

Now you're asking about cultures - those are buried under the sands as well. Most of the spectacular finds from the Green Sahara period are at paleo-lakebeds: each megalake was a gathering point for all sorts of animals, including various human cultures. One such site is at Gobero, Niger.

Green Saharans were hunter-fisher-gatherers (and by the mid Holocene had become pastoralists), and while this doesn't sound like much of a "civilization" compared to contemporaneous Gobekli Tepe, Catalhoyuk, and Jericho - it was still a complex and fascinating series of cultures. Gobero hosts the earliest cemetery in Africa, beginning with the HFG'er Kiffians and lasting into the mid Holocene pastoralist Tenereans. The Tenerean burials include a man interred in a sitting position on top of a turtle shell, and a triple burial of a family who were placed together in an intentional and intimate position. Here's a National Geographic piece about Gobero with lots of pretty pictures, and Paul Sereno and company's paper on their excavations

There's a whole other side to this question which you probably wouldn't expect - There's actually a good amount of things which aren't hidden at all. This is primarily rock art, the earliest of which is the Apollo 11 Cave in Namibia which is dated to ca. 25kya from associated charcoal. Now it wasn't hidden by sand, just hiding in an extremely secluded cave for 10s of thousands of years. So, okay, sure, it's hidden.

This is an ultra rare find, and there are only a handful (or less than a handful) of examples of pre-Holocene rock art in Africa, it was most likely being done but has been eroded very effectively by Africa's brutal iconoclastic environment. The majority of rock art is from the mid-Holocene thru today, so actually I'd say the majority of what the Green Saharan cultures left behind is their uncovered artwork.

The most spectacular rock art sites are from the Sahara, mainly in a mountainous cluster in the central Sahara centered around Tassili n'Ajjer. The two early periods of this rock art are called Bubaline and Round Head: Bubaline art is almost all engravings of large animals and is found across the Sahara, whereas Round Head art occurred mainly around Tassili n'Ajjer and shows strange faceless figures with, well, round heads. Bubaline art is amazing, it's often realistic including the notable life-size engraving of a giraffe at Dabous, Niger.

Round Head art is by far my favorite period, the figures are radically not what you would expect from rock art. They aren't stick figures or even large local animals – scenes show lined up groups of round headed figures with no faces, life-sized figures with multiple strange protusions coming from their head, people riding undomesticated sheep, and even a floating blob with tassels (all of these have a completely unknown significance). The British Museum has a wonderful series online on rock art, and here in the Algeria section you'll see one of the mysterious Round Head panels, as well as art from other periods.

Round Head art was certainly not just painting what you see but was something else entirely, presumably it held some kind of spiritual significance to its painters. Round Head art was done at “stone cities” which are outcroppings of rock which form a series of clustered “towers” onto which people painted. It is no coincidence that such unique art was done in such a unique place, likely Tassili n'Ajjer was a cultural locus for regional tribes who used the site in a similar manner as bronze age Britons used Stonehenge. Read all about it here in this book about Round Head art by Jitka Soukopova

Making rock art never stopped with the end of the Green Sahara, the most recent Saharan culture to make art are the Berbers who left both art and their written script. South African rock art done by the San people has been going on from the early Holocene through the 20th century Reference.

But the original question regarding “civilizations” has not been answered. As EvanRWT mentioned, your typical urban metal-using hierarchical proto-state is only going to be found in Egypt. So if you were wondering what style of cultures existed in Africa during the Green Sahara period, the answer is simply hunter-fisher-gatherers and pastoralists. As the Green Sahara ended it forced people throughout the northern half of the continent to change their way of life. Domestic animals, which had occurred in the mid-Holocene, become a more central part of life for many people. Through the late Holocene, many HG'er traditions were usurped by migratory pastoralists fleeing the desiccating Sahara.

As the Green Sahara ended, it also closed the trade networks which had connected Saharan Africans to Nilotic Africans, this happened just as metalworking was spreading across the Near East (and into Egypt) and changing everything. Before the closing of the Sahara, there's not such a huge material gap between settled Badarians in Egypt ca 4000s BCE and nearby pastoralists (but there is some difference). That small gap in material cultures became a huge chasm during the bronze age, so that by the mid 3rd millennium BCE various kings of Egypt were building megalithic pyramids and sending armies into foreign countries, as nearby pastoralists in Laas Geel Somaliland were living a semi-sedentary tribal cattle-herding lifestyle making rock art, as their ancestors had done for the last few thousand years.

But, it should be said that the Egyptians in NW Africa were not the only late Holocene urban culture to arise from the ashes of the Green Sahara. The other notable urban center would be in West Africa: the Tichitt Tradition. It appeared in Mauritania around 2000 BCE and was made up of pastoralists who had decided to settle down. These people built dry-masonry stone “houses” which were actually multi-family compounds, and lived in defined villages. These people survived until the early iron age when Berber invasions from the north led to the culture's collapse. Source

As EvanRWT stated earlier, it's very unlikely that another urban civilization is going to be found in Egypt (or even probably in northern Sudan). That being said, there has been considerably less archeological work in west Africa, and the story of the Tichitt Tradition is by no means complete. In my humble opinion, I think there's probably a lot more going on in west Africa during this time that we know about – there's certainly a connection between the decline of the urban Tichitt culture and the rise of the Tichitt-Walata culture (Proto Imperial Mali) and the Nok culture (Proto Yoruba) in Nigeria a few hundred years later. Pastoralists also fled to central and east Africa, possibly they too invented urban traditions in response to their new environment. We don't know simply because those countries are woefully underfunded in archeological research.

So to answer your question: the only urban civilizations which existed in Africa during the Holocene were in the later period in Egypt and Mauritania. Prior to that there were hunter-fisher-gatherers and pastoralists throughout Africa, from the Capsian culture in Tunisia to the Proto-San on the coast of south Africa. Whether you'd like to call them “civilizations” or something else is up to you, as that term says more about the speaker's opinions than about the cultures themselves. Holocene Africans left tons of material behind, yes buried in the sand. But mostly they left exposed rock art, which has its own panoply of issues related to accuracy in dating, preservation, and our ability to understand its significance.

hi! this may be worth x-posting to an archaeology sub, e.g. /r/AskAnthropology, /r/AskScience, or maybe /r/Archaeology (not an "Ask" sub)