There's a couple of parts for VAAI - one is the HardwareAcceleratedMove (the function for Clone, Copy Templates) and a separate part called ATS (Atomic Test and Set. The ATS part is the one that handles the reservation locking for the Data Stores/LUNs - this needs to be enabled to prevent SCSI Reservations from running. Take a look at KB 91644 - the introduction sections talks about ATS and its importance. You should disable the HardwareAcceleratedMove part of VAAI, but leave the ATS part enabled.
As for the disk replacement, I would recommend that you do replace the disk - all indications are that the disk has failed. I can see where someone could get confused when looking over the older cases as it appears that the disk was not replaced as the same serial number is still there.