Maybe you're thinking of Great Zimbabwe? It wasn't destroyed or covered up but when it was discovered by Europeans in the 1870s, archaeologists went to great lengths to explain how it was built by anyone but the local Bantu. It had to be Arabs or Phoenicians or Hebrews, because in the colonial mindset Africans couldn't possibly have created something so obviously 'civilised'.

I agree that the idea that archaeologists actually destroyed evidence of African civilisations sounds dubious. The archaeologists of the late 19th century might not have been the most ethical bunch by our standards, but they weren't that bad. As with Great Zimbabwe, they'd be more likely to explain it away as being built by non-Africans, or simply ignored it. There also wasn't a great deal of archaeological work or archaeologists in Africa in the 19th century anyway.