It could be, but I doubt it somewhat as I've deleted the MediaMonkey folders in the past as well. As I won't do that no more I'm not sure what the cause is, will have to keep an eye out.

Then I would maybe point to the fact that MM "thinks" the files are still there, if ones previously synced are on the new sync list.

Manually from phone.

How are you emptying the device? Manually deleting the files via the phone or MM? If the files are manually being deleted, then MM may still be seeing these files in the database (on the phone) or on the "synchronized" list maintained on the Windows client and thus thinking they're still there and not needed to be re-synced?

Well, I guess a better question would be while it may say "Syncing 23 of 47 files" (instead of the 50 contained on the playlist), are all 50 actually present on the phone after the sync?

No, as I cleared the device of files prior to sync.

Is it possible that the few that y is short of happen to be files already contained on the device?

I often sync to an empty device a Playlist of x files (it's limited to x files so there are always that amount of files on the Playlist). However MMA reports it is syncing x of y files where y is often a few files shy of the expected amount.