We had an issue that plagued us, and I'll explain the fix so that hopefully noone else will have to go through the existential hell we did.
On our 4.5 build, patch 3 of ePO, the master repository got wiped out when we tried to check in any new package. We would pull in a new catalog.z from a mirror build which would temporarily fix it, but upon a new package check in , it would wipe it out again. As in all packages are gone and you see an empty white space on the master repository page. Not pretty.
In the epoapsvr.log we saw the following error: ERROR: error, more than one keyset as master repository key
We deleted the extra keys we saw in the ePO console, and it seemed clear that a new key that we had created was master. Yet, the problem persisted. We then troubleshot a bunch of other stuff.
Content in the %installpath%:\programfiles\Mcafee\epolicyorchestrator\db\keystore turned out to be the fix. There were multiple .zip files in there, that were legacy from previously existing master keysets. Normally, according to our understanding, their presence there would not be a problem. We think that in this case one or more of them had become corrupted. We deleted all but the one that corresponded to the current master key: sm<master agent / server communication key name>.zip.
This cleared the problem. Hope this helps someone.