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Thanks for telling us about this. I was not aware of this kind of behavior. Right now, you can’t disable certain file exetensions from automatic encryption but it’s a good feature to add regardless. There are similar situations, like .gdoc and .gsheet where this probably will come in handy.
It’s a fairly simple thing to fix, so we’ll be adding it shortly (with a set of built-in extensions for now, it’ll be user-editable later). You can follow this at https://bitbucket.org/axantum/axcrypt-net/issues/334/add-a-list-of-user-extensions-to-be .