Ah, ok that makes sense.
So, I didn't install eq2 maps separately, I've just been having profitui handle that too. It appears after you add that file to the ignore list you also need to tell it to skip updating the eq2 maps ignore list as well, otherwise it will want to overwrite the changes to the ignore list lol
Not sure how you're verifying files, I'm assuming you're doing a hash, might have it check either with yours or their hash for the file in the updater depending on if you have the setting "Update EQ2MAP when you start the utility" checked or not, or don't download that one while updating eq2 maps if it's checked off.
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