[Krsqk]

You can avoid most of those weird effects by adding any new components/facilities/hull sizes/etc. to the end of their respective files. The game seems to store things by position number, and this preserves the number for old items. Come next major Version, you can rearrange things into their proper positions.

I'm not sure if this works for components in the same family (i.e., adding 2 levels to ECM); it may cause problems with upgrading.