when i do a bulk archive, it will sometimes put 2 copies entries into the archive file. it is more likely to occur if i am archiving more tasks. at times, it seems certain entries do this repeatably, but i am not sure.
there are times when i think i have reset everything (git is clean, archives are moved out of teh way) but this still occurs. i cannot make an mwe but it seemed worth reporting. where is it getting the duplicates from? idk. it has to be either the source .org file or the newly created and written archive file. idk if there are any caches or text properties or some hidden stuff in the agenda. but i can tell you that there have been times when i experimented with not cleaning everything and the duplicates increased. each run would create a new duplicate of certain entries. btw i have been trying to archive tasks to files for a year now. it is too slow for me. so i hit on the idea of moving archives out of the way, then archiving a little at a time to new archive files, then using the shell to append the new archived entries to the old archive files, then moving the old archive files back. thus, this isn't an issue of big archive files. wish i could provide more for you or even figure out debugging but i cannot; just hope it will ring bells.