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It probably looks at the txt file version on your computer and compare it to the version specific on the addon page. If they are the same technically it shouldn't overwrite, especially if the date on your copy is later than the on the download page if it checks that as well.
If you are that worried, test it out by making a copy of your one and see if it overwrites your changes when
1. You leave the app's version as is
2. You change your copy to a slightly higher version to let minion know your's is more up-to-date.
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