Grayed out are overwritten
The mod enabler gave the warning about file conflicts and then grayed out the mods that are overwritten. The whole mod isn't overwritten, just the files from the warning message.
If things are overwritten, you will see the latest change. The grayed out mod will return when you uninstall the later mods.
It's like overwriting a document in a word-processor with another document of the same name. You get a warning. The good news is our mod enabler keeps a copy of the old file for you. It isn't lost.
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