The CRA's never EVER report anything to anyone, much less reporting to each other. Think of them as 3 completely separate entities who don't know each other exist.
Yes, you will have to dispute anything you want changed separately with each of the 3.
As to why your TU score went down, it could be many reasons. If all else the same, you may have been re-bucketed to a better scoring group, one with no negative items. Now you are being scored against others with clean files.
How old is your oldest TL? Est. avg age of accounts?
Just keep paying everything on time, do not close positive accounts and you will see your scores continue to rise.