I'm having a similar issue - I had installed the 'Fores New Idles In Skyrim' and 'SKSE 64' tools previously in my mods manager, and have since removed both. I can see the option to remove them from my Tools dashlet, but they never actually get removed from Vortex. I get an error about FNIS all the time, but can't seem to completely remove it.
Am I missing something? Is there a way to check if it's still installed somewhere?