Well it certainly didn't help, but it's not the sole or even primary problem. Obviously an army of angry Greeks torching Persepolis resulted in the loss of some knowledge and the subsequent abandonment of the site saw to even more losses. That said, I think the modern population of Hamadan not wanting archaeologists knocking down their houses and excavating their basements is an even bigger contributor. Hamadan is the modern name for the ancient city of Ecbatana, which was one, sometimes the primary, capital city in the Achaemenid Empire. The Bible (specifically Ezra 6) suggests that there was a royal archive there or at a nearby palace and common logic based on other sources would agree. Persepolis had no walls, little to no pre-existing infrastructure, and an economy entirely based on being the palatial royal capital. Ecbatana on the other hand had been a full fledged city on major trade roots centuries before Persepolis was founded.

The Achaemenids operated a system of multiple, seasonal capitals with different specific functions. Persepolis was founded by Darius I as an expression of royal power and grandeur, not really as a city but as a colossal palace complex obviously a lot of it's records were lost due to Alexander. Ecbatana was the first imperial capital after Cyrus the Great conquered it when he defeated Media and remained one of the primary capital cities for the duration of the Empire and has lost many of its ancient features as the result of continuous habitation. Any that remain tend to be hard to find because their are people living above them, but there are other cities, each with its own problems for finding sources.

The earliest city associated with the Achaemenids is Anshan, one of the two even more ancient Elamite capitals which had been taken over by Cyrus the Great's ancestors. Anshan seems to have been abandoned in favor of Ecbatana, Pasargadae, and Babylon and allowed to dwindle even in Cyrus's time. Another 200 years of abandonment and the fact that it was only briefly associated with the Persians mostly rule it out as a place to find sources. Cyrus built Pasargadae as his new palatial complex and home to his tomb. It is also usually regarded as a capital, but much like Persepolis it's really just a big palace complex and we don't really know what it's role was outside a few ceremonies. We also don't know why it was abandoned and destroyed, but also like Persepolis there is evidence of fire, this time around 280 BCE which would have destroyed the records there (and there probably were fewer to begin with).

Finally, at least in Iran, there's Susa, the second Elamite capital, which Darius I returned to prominence when he built his palace there. This was the second major city in Iran to function as a capital, but like Ecbatana, it has been continously inhabited and ancient records and buildings suffer the consequences of that. Darius' palace has yielded several notable finds, but the whole city of Shush, Iran cannot be stripped down in search of Achaemenid records.

Beyond Iran, there's more to work with. Babylon was home to an imperial treasury and archive and also often functioned as another capital and Babylonian finds actually yield some of the most extensive records from the Achaemenid period. Sardis in Anatolia and several cities in Egypt were also important imperial centers that would have kept a written record and indeed both regions have turned out important inscriptions. Whether any of these properly count as "Persian" sources is up to you, but they are certainly non-Greek sources for the Persian Empire. In general though, the history and conditions of important Achaemenid sites have not been conducive to preservation.

Despite all of that, the absolute greatest problem with Persian sources has llittle to do with location, and a lot to do with papyrus. Achaemenid rule saw Aramaic, usually written on pressed and woven papyrus fibers, become the lingua franca from Anatolia to India. Papyrus became the primary medium for written records, replacing stone or clay tablets in most instances. The problem is, Papyrus becomes very brittle very quickly and is prone to crumble or decay if not stored properly. When there were still people to regularly copy important records over to a new page, that wasn't so bad, but when the Hellenistic kings stopped maintaining Achaemenid records, the papyrus crumbled away or burned. Even in the great and ancient centers of literacy and written records of Mesopotamia and Egypt, local record keeping shifted to Papyrus as well, meaning there are actually fewer surviving records from the Iron Age Persian occupation than earlier Bronze Age kings who had everything put onto clay and stone. Papyrus just isn't a great long term storage method for information.

A related and similarly technicalroblem also stands between us and ancient Persian records: the Persians just didn't write the sort of things that their Greek successors wanted to read. We don't have any ancient Persian epics, plays, narrative histories, ethnographies, or poetry from the classical Persians. That's not because they didn't exist or because they themselves weren't interested in those topics, but because anything like that seems to have remained an oral tradition among the Persian people. Like many societies before them, the first usages of written language among the Persians were for record keeping and monuments. In his Behistun inscription, Darius I claims to have commissioned the first Iranian written system to create the Old Persian script, so literacy was phenomena that occurred during the imperial period for the Persians. Thus, oral traditions persevered and the written record is either limited or confined to record keeping.

That said, this brings is full circle back to Persepolis because, despite everything I've said so far, Persepolis is where archaeologists found the greatest cache of sources from the Achaemenids. The Persepolis Fortification Archive and Persepolis Treasury Archive together consist of tens of thousands of clay tablets and fragments, mostly written in Elamite with a fair amount of Aramaic and some other languages mixed in. These tablets contain rations, payments, deliveries and other clerical records, largely from the reign of Darius I, with a little from Xerxes I and later kings too. The Persepolis Archives have been crucial to developing a better picture of day to day life and the business of running an empire in southern Iran outside of the Greek perspective and survived in spite of the city's destruction.