How could two identical HDDs with identical content have different amount of free space?

I have HDD1 and HDD2. I use the second one as the backup of the first one. Both of them are the same brand and type (Toshiba 3,5" 2TB HDD 7200rpm), I purchased them together. I use Windows 10 Pro x64 with latest updates and drivers.

I use FreeFileSync for backing up (syncing) my data to the second drive. I synced everything today twice and FreeFileSync tells me everything was synced successfully. No difference between the drives.

However the first one has 400GB free space on it and the backup drive has 500GB free space!
- I emptied all Recycle Bins
- I re-synced with FreeFileSync (still tells me there's no difference)
- Checked even the contents of both drives (SHA-1 check with Total Commander). It also tells me everything is the same on them.
- Scanned both of them with Windows CHKDSK. No error on any of them.
- I defragment both of them regularly (last time today). Zero fragmented files on both of them.

Any ideas? How have I lost 100 GB of free disk space on my first drive?

Maybe your recycle bin was corrupted. I had a similar problem between 2 disks, same number of files, occupying the same amount of space... but 40BG lost between 2 identical disks.