(You don’t need to upgrade your setup to this version, just downloading it and running it with those parameters should produce a couple of tables of information)
D:\>syncthing debug database-file tnhbr-gxtuf TreeSizeFreeSetup.exe
syncthing: error: no such folder
D:\>syncthing debug database-counts tnhbr-gxtuf
syncthing: error: no such folder
I guess in that case it most likely means that the --home is not the path to where the database (index-v2) is stored. I don’t know how the portable thing is set up, sorry.
The problem here is that there is a sync conflict between two versions of the file (scanned independently on two different devices). One of them wins, but the losing device is apparently not online to resolve it at the moment and the conflict remains. No problem so far.
Once the file is deleted, however, it is still in conflict with the old version from the offline device and now we resolve it differently because in a conflict between a deleted and a non-deleted file, the deleted file always loses.
This obviously results in incorrect behaviour in this case.