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Nothing can remove warded blocks besides the person that put it or someone in creative. The way they work is that they check to make sure they are still there so worldedit is removing them, but then a tick latter the server replaces them.
Yeah, wardstone and wardglass are special items that require more data to work than WE messes with. Basically any non-vanilla block that has some form of usage restriction will be a no-go with WorldEdit.
