Many moons ago on a deposit made at BofA branch on a Friday, the full amount was reversed on Monday. Called customer service first to file a report. Then trotted down to the branch to find out what was going on. It turned out they just changed to a new scan system and apparently it failed to properly scan the very fainted WM MOs - all the MOs still at the branch as they normally would send Friday's checks together with Monday's to processing center in MIA.
At first the teller manager said since customer service already had a case opened, I could just wait for the resolution. I said that was ridiculous - I aint going to wait for 2 weeks to get my multi thousands deposit clear while you were holding my checks right there. He started calling around. About 4th call he was directed to, a special research unit in CA and the investigation finally got started. By end of the day I saw the items were reversed back to a credit to my account. Shortly after 4pm the teller manager called to inform things back to what they should have been.
Since then I always check online the following days after depositing items. It is not uncommon that the credit was not processed the same day but next day. However, the fund was made available in the balance despite it was still a pending item. So I just let it be. The annoying thing though, is whenever this happens, the image of the check is forever lost, so as the details of the deposit slip. So you do need to keep your deposit slips in good order just in case you need to go back to refer them,