I'd initially suggest unlinking, restarting SSMS, then relinking. This may clear up the problem.
If not, and you are still seeing drops on the Commit tab, then you need to use the "Undo Changes" option (see here
) to update to the repo contents.
Restoring a linked database is generally a bad idea as it alters much of the database without SQL Source Control "knowing", and leads to the sort of problems you're seeing.
It's preferable to sync either with a get-latest if everything is in the repo, or alternatively using SQL Compare/Data Compare which should help stop everything getting out of sync.