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You're wanting to "legalize" a Pokemon directly in the slot via the right click context menu; no, the plugin does not add that functionality. If you're wanting to edit a Pokemon, you load it to the editor then run whatever edits on it.
As for retaining values and only fixing what is wrong -- you're misunderstanding the intent of the plugin, which is to obtain battle legal Pokemon. Originally the plugin tried to do what you're wanting, but applying "fixes" to whatever is wrong is not foolproof and has tons of considerations that need to be accounted for. It is MUCH simpler to just find an encounter that can have the moves, generate it, and set it to the requested level and stats. If you want to pick and choose properties to copy over to the original, that's on you.