We've been having this happen to us as well. It's been intermittent, and nothing that seems to have any sort of pattern to it, but I will have doctors saying that their prior note is not in the EMR.
We just noticed this again today. We did an office visit note that was pretty lengthy (due to medical clearances needed), and I know the note was completed at the time of the OV because the schedulers will copy/paste the "plan" part of the note into the scheduler, but now that the patient is here for surgery, when we went to review the office note, it was not there.
If it ever came up, how would I explain this to someone requesting a copy of our records (i.e. insurance company, attorney, other physician etc.)??