They should stay put because the game installer doesn’t know about all the addons you have installed, so it can only remove what the game came with. It’s easy enough to back them up though. I always keep a copy of WTF and Interface with all their contents in case a bad addon or WoW update breaks something. Makes it easy to quickly fix. Just make a folder called “WoW Backups” or something like that wherever you want to keep it safe and copy the WTF and Interface folders to it.
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