We try pretty hard to make sure MekHQ continues to load campaign files saved from older versions, so it should be fine going forward. I'm not aware of any changes since then that would affect this. I'm don't have the code in front of me right now but I suspect it applies the acquision limits when presenting the alternatives for refits. You're correct that this should not affect the ability to reconfigure omnis, but from what I remember of that part of the code the fix will take a bit of work.