This sort of depends on how you're defining "genocide." It's entirely possible that, in the ancient world, for example, entire peoples were wiped out by another people. While it's by no means a historical document, God's command to the Israelites to destroy the Canaanites shows that the idea of systematic destruction certainly existed. However, that this people be wiped out without a trace is unlikely. People leave artefacts and bones behind. What's more possible is that a society could be destroyed, but that the exact reasons for why are unknown.

Once again, though, whether or not this is a genocide depends on your definition. The modern definition insists that there must be intention, and that without that intention, it's not a genocide. However, what "intention" is is as debatable as anything else. Even if it weren't, I'd argue that it's certainly possible for genocides to have occurred in the ancient world and later, or at least mass murdering and relocation actions that were done with the intention of destroying a people.

I think there examples out there that make your premise plausible. Of course, it would be impossible to make any conclusions when an event has not been recorded, or the information has been irretrievably lost.

However, if I may bend your premise. What about events that had been recorded, but have only recently been re-considered through the lens of genocide? That is actually something of a hot topic in academia right now, especially in considering settler colonialism and its interaction with aboriginal peoples.

For instance, Mohamed Adhikari argues in his book The Anatomy of a South African Genocide that the actions of the Dutch East India company and later British colonial administration in the 18th and 19th centuries constituted genocide against the Cape San peoples. In the book, he describes a cycle of settler encroachment on San territories, San raiding in retaliation, and violent settler retribution. To intent, he points to a 1777 policy statement by the VOC that sanctioned the eradication of the San.

If we take a broader view, historians of the Australia are also beginning to explore settler-aboriginal interactions through the lens of Genocide. A book that explores this are Genocide and Settler Society, which is actually a collection of essays edited by A. Dirk Moses. The central premise of the book is that frontier violence in the period before 1900 constituted an attempt at the physical extermination of Aboriginal societies. But also, in the years after 1900, the taking of Aboriginal children to be assimilated into Australian settler culture constituted an attempt at "cultural genocide". That is, an attempt to alienate generations of Aboriginal peoples from their traditions and customs, so that those traditions and customs would be lost or erased.

Of course, such a history has some parallels with North American interactions between white Americans and Canadians, and the First Peoples of that continent. There would seem to be enough parallels that A. Dirk Moses later assembled a collection of essays for Empire, Colony, Genocide expressly as a piece of comparative history, tracing the similarities of Australian, North American, African, and even Ottoman and Russian imperial projects.

To sum up, I think that there are lots of events that could be counted as "unknown genocides" in the sense that the concept of genocide had never been applied to analyze them before. When such a theoretical lens is applied, a case may be made for genocide, given certain definitions of genocide.