I don't use Axe's tlk editor because of that repair function, which is obviously bugged.
I don't know if/where those resfrefs are used, so can't answer your questions. But I can suggest a great tool to edit tlk files:
http://nwvault.ign.c....Detail&id=1295
It can export/import text files, so you could probably fix your resref problem by exporting both original and modified tlk to txt (including blank rows) and use some kind of diffing tool (winmerge?) to compare these two versions and then bulk copy unmodified lines with sound ref's and fix what remains. It all depend on how many changes have you made to original tlk though.