Itemsadder has its own file in map files, called region (so there are 2 region files, one in world -> itemsadder -> region

This causes many issues with chunky, for example trim or fixing light data is impossible, when I remove itemsadder and this file, it works fine.

This has already been fixed in a newer version of chunky. I am assuming you are using an outdated version.

I will not be adding specific support for plugins; really this is an ItemsAdder issue anyway as they are storing their plugin data in the world folder (and especially files that look like region files) which will easy confuse other plugins scanning for the vanilla files here.

If you're still having issues with this, try updating first to the latest version of chunky, and join the Discord support server if you have any questions.