I have now had several instances of the ftb app not removing mods that it was supposed to. I remember it working at some point. I believe I started having this issue after downgrading the direwolf20 pack and then re upgrading it. After that it failed to remove minetogether from 1.1 to 1.2 and it failed to remove performant from 1.2 to 1.3. Ive also now discovered some duplicate mod files in the mod folder of different versions.
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