Assuming that you have hundreds or thousands of files and a manual comparison would be too time consuming I would create an SSIS Package using a For Each Container and load the list of physical files into a Temp Table then use a Left Join between your two tables to determine the delta.

If your table is set up correctly, with constraints on the file name, you could probably get away with doing an insert directly into your table. Those that already exist will fail, those that don't will succeed, agian doing this in a For Each Container in SSIS.