The warning message means that the new mod wants to change something that has already been changed by another mod. While something really bad is possible, most of the time the worst that can happen is that something in the earlier mod won't work anymore.
The best thing you can do is copy whatever the message says and post it here. There is always one of us who can tell if it's a bad thing or not.
The biggest one to watch out for is 'Menu.ini'. This will change something central to the game and has a good chance of overriding something you don't want changed.
The one you don't have to worry about at all is 'Readme'. They don't show up in-game anyway.
As for things that are greyed-out, I don't see why that's a concern because those are mods you've already overwritten. All 'greyed-out' means is that you can't uninstall those mods without uninstalling something else first, and if you try to uninstall a greyed-out mod JSGME will stop you and tell you what those others are.
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“Never do anything you can't take back.”
—Rocky Russo
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