Reinstalling windows alone shouldn't remove applications or data, note I said 'shouldn't,' but I have no idea what the PC Shop did so can't speculate. Remember I started the point you quoted with If they aren't there it is possible and 'possible' being the operative word as I simply don't know what they did.
If there is nothing in the virus chest infected files section they are gone, history, kaput. There are tools that can recover deleted files, google search, (and we don't know what happened to these files), these however aren't very successful and less so the longer it is after deletion.
Even if they were 100% successful any recovered file is likely to be in fragments and in the case of files from the chest encrypted so the success rate would be even smaller. Again even if possible what would you want files back that were detected as infected, it is plain crazy, sorry I can't sugar coat it, that is a reality.
So those files that were in the chest are of no value whilst infected and if your system is working fine there loss isn't really an issue, unless there is something else you haven't mentioned.