I think the problem may be that you are giving credence to message board blather.
The major brokers have decided to request certs for all CMKX shares held by their clients. This alone should tell you that your shares are backed by the master cert held by CEDE and your certs will be along in due time. You are making up a problem where there isn't one.
When CMKX was revoked, all regular short positions were wiped out because the short was against borrowed shares and since the stock price has dropped to zero, they don't have to be covered. The shares they were shorted against are still in the accounts of the longs.
I know you are referring to the supposed naked short but there is no evidence that it exists and there is even documentation that it doesn't, at least as of the end of April and none has surfaced that would indicate one has been created since then.