The tldr is (unless there's more info missing) it's an issue if either:
1. you have a custom install path (iirc you can set it to download to your custom path, but it might not default to your custom path)
2. you don't delete old versions of mods that don't have a version number as part of the file name prior to downloading the updated version (or if you don't clean out old versions of mods in general, I remember something about unchecking mods being unreliable, but I haven't confirmed)
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