IC2 or Experimental (IC2E) and IC2C are yes 'IC2' but are separate mods still and yes will likely have separate IDs used, I can't say there is a way to have things be exchanged without encountering items and so on being removed, I can't say if it is possible by hand with each ID being exchanged but I'd say just start a new world or stick with IC2 is the way to go to save you the trouble.
Someone might know more than I do but to me it seems like a tricky thing to do that isn't really worth the effort.
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