Of course, the easiest thing is to just look through your edits, and compare your edited files to the originals, both of the mod and of Stock, and see if you have some assignment aspect that you edited that is now "off". Compare your ranks to what's allowed. It might be that you have to have at least one seaman, and not have everybody at PO level or higher...
If you want to experiment (possibly a waste of time), you could copy the entire game folder structure - including the Save folder, to another area of the hard drive and by use of
MultiSH4 v1.5, have a lab rat to mess with, and not goof-up any further the career that you have. I'd check your edits real close though. I don't think you'll be able to recover what you had as far as the current campaign goes, but you might be able to go back to a previous save where you had all the crew slots visible, and continue from there again... maybe. You never know until you try though. Just make copies of things...
Another thing, there might be crew assignment changes included with that new conning tower you got, so that'd be another place to check. You may have missed a file, and it overwrote a portion of what you did.