This is designed similarly to removing symbols; each section gets a unique id, which is used to map symbols to sections through removals/additions, which is then mapped back to proper sequential indices when writing out.
Compared to removal of symbols, section definition symbols add a bit of extra code, as they contain section numbers in the section aux data as well. For associative comdat symbols, that needs to be updated just like the normal section number.
I've tried to keep the removal behaviour sensible, that is: When removing a section, all symbols pointing to that section is removed. (This matches GNU objcopy.) If there were relocations against those symbols in a section that is kept, writing errors out. (GNU objcopy on the other hand will just leave the relocation pointing at any random symbol that is left, but I prefer erroring out in this case.)
If the target section of a associative comdat is removed, the associative comdat can also be removed automatically (as nothing would include it). Nothing that really is used in the wild I guess, but makes the case of manually removing a specific section more convenient.
Can you keep the RUN sections together?