You passed your state's MPJE?
No. If there are serious unacceptable discrepancies, you inform the Board or the DEA within the time period. I'd recommend that if you don't have an accountable PIC, another pharmacist serves as second. In cases of discrepancies, that is a DM problem if not a regulatory one. Depending on the state, you are supposed to refuse the PIC should there be reportable discrepancies until they are accounted for either internally or externally.
By the way, based on what you say, probably not, but you have to update the books as the baseline inventory unless you're in a state crazy enough to have a 100% inventory in certain ones. You should re-read the DEA manual and the state CSA again for permissible filing.