file synch conundrum

[footfootfoot]

There's probably not a simple fix to this problem but here it is:

I have most of my music on my desktop hard drive D: at some point I copied/backed up my library to a passport drive and began using that for a few months while I was in transition. I realized that it would be nice if I backed shit up properly but saw I had created a problem.

F:\My Music has ~ 49,000 files that have been mostly cleaned for dupes and junk but has maybe 5,000 new files on it.

D:\My Music has the same~49,000 files though not cleaned for dupes and junk and may have a few hundred files uncommon to F:\

If I use D: (the older drive) as the source it will put a ton of crap back onto F:, If I make F: the source it will add the new songs to D: and delete the junk, but what about the files on D: that are not on F:?

I already have a headache.