Depends. Where the TD *was* looking, or where it is *now* looking? And where the TD *was* looking also depends. Which is another reason why moving this to a known, "approved" location makes sense.
The player database is stored in multiple files, but the index is in only 1 file. So, if you've got the index file (td.db), then it should show all of the players in your database. If you don't, then it shouldn't show any players in your database. I can't see how it would get all players except for 2.
As for tournament files, if you know where the "missing 2" files are, copy them to the folder "My Documents\The Tournament Director 2\Data\saves".
For the missing players, you can load a tournament with those players and press the "Add All to DB" button on the Players tab. This will add them back to your database with the proper internal ID. If you had additional information on these players (like address, phone, email, etc), you'll probably have re-enter that info.
Are you attempting to run Stats and not seeing what you expect? If so, you'll probably have to change the "Tournament File Locations" on the Preferences tab. This needs a better solution, because it defaults to the "saves" folder in the install location, which is incorrect. I'm thinking I'm going to do some updates to Filters to allow them to include file paths, instead of having a simple preference on the Preferences tab, so I'll fix this up with that addition.