A particular problem is anything that modifies XML files: either the modded version containing out of date info will be loaded or the new one will be prioritised which doesn't include the modded stuff (I don't know in enough detail how the game decides which to load) so the changes added by the mod need to be re-merged. I just did mine using context diffs which went smoothly enough (well, ish: one of them needed to be done manually) but until anything that makes similar changes is updated it won't work...
