Clean up not only removing ineffective kerning values?

Using the Kerning-Window, I copy-pasted Groups and Kerning pairs from one of my older Glyphs-Files to a new one. Because the new file contains less characters than the new one, I used the “Clean up” button at the lower right corner of that window. This resulted in 30% less lines in the Kerning Window. As I was curious to see what had happened, I used “Edit –> Compare Fonts” and was surprised to see that “Clean up” not only “removes ineffective kerning values, e.g., leftovers like kerning entries of letters that are not in the font anymore” but also kerning pairs that are valid. Is this a bug or what is happening here?

I also had this impression, but did not investigate it further for lack of time but decided not to touch that button anymore for the time being. My impression was that kerning exceptions were purged in the process.

Thanks, that could make sense, but removing exceptions should rather be an option, I think. Especially as Compress is said to do such a thing. And even for “Compress” I would like to be able to choose between “Compress and remove Exceptions” and “Compress and keep Exceptions”.

“Clean Up” did not remove exceptions. I still have no idea what “Clean Up” really does …