The pilot files have a once-off conversion process which should transfer campaign progress. It doesn't alter the 3.6.18 files which is why they look fine when you go back to 3.6.18. However, the conversion only works for a single campaign, only for the active mod, and if there are any issues with the 3.6.18 pilot, or if there's a bug in the conversion process then progress will be lost.
So, for your "blank" 3.7.0 pilots, try deleting the .plr & .csg files in data/players. Then, activate the mod that you want to keep the campaign progress for and run 3.7.0. If the pilots are still missing campaign progress after doing that, post them here.