I tried chkdsk but it didn't show anything not normal.
Yes, those are HDDs.
> if its only a mirror, then why not just wipe it and re-synch?
Because it's >1 TB of data and both drives are connected only by USB 2.0.
No "File History" in use here.
WinDirStat finally helped me find the issue: a file with a >4 GB size only had a "size on disk" of a few MB on one drive but >4 GB size on the other. So weird! A similar finding with a >1 GB file. Now both drives have the same available disk space again! The file synchronizer might have an issue with larger files, I'll keep an eye on this.
Thanks for all your help!