Many years ago, I had the physical copy (still have it) of Tie Fighter Collector's Edition and I got pretty far until I got stuck on a mission in the expansion.

If I get this game on gog or Steam, will I be able to use my old save file as I would like to continue where I left off? I would put it in the saves folder.

Yes (I was able to do it with X-wing vs Tie Fighter Balance of Power), the pilot files should be unchanged (just remember to use the save of the Dos CD rom with the DOS cd-rom and windows CD rom with the windows cd rom) though I strongly advice to get the GOG version, in my experience Steam can be more problematic with older games.