I've been saving up all my credits. I'm at level 23 now and I'm going to replay all the missions to get the achievements. Will the upgrades I buy now apply to the missions I replay? Will any of them? Some of them? How doe sit work?
When you replay a mission you only have the upgrades you had the first time you played through
As @Raven pointed out in the comments in the branching missions if you replay the other path you'll have all the current upgrades. When I finally got around to playing Safe Haven I had battlecruisers already.