If you have several files, just look at them all and decide which of them is the MOST accurate and delete the remainder.
OR, you can combine the BEST of each and delete after that. It is not important WHICH tnsnames is being used, but it IS important that it have the correct connection parameters. So, just look at the files and compare them to the others and then clean them up. No biggie.
also, Toad will use whatever tsnnames file you have in there. It won't matter if you change/update/edit one of the files as long as the connect string remain the same.