The first thing I would do is consider my back-up and recovery strategy to protect data I don't want to lose. The inbox is the one most likely to corruption/deletion (not just by and AV), mainly because it is the one open if you have any computer crash/problem.
So the Inbox shouldn't be used as a general storage folder, more of a pending tray in an office, when read it is actioned and filled in a folder more appropriate to its content.
The scan that would check those email database files is the on-demand scan and the Program Setting, Exclusions, Add is where you would input the path not to be scanned.