I wouldn't worry too much. you might only make the drive heads dirty and that can be cleaned. anyway the FDD is replaceable.
still, maybe it would be a good idea to use external FDD for checking diskettes. otherwise, you should inspect each one of them visually.
BTW, there are hacks on aminet for using PC FDD as external Amiga drive.
hm, you might even use PC for testing, there are 'hacks' like the one that needs two drives.