My character has a dirty "Fortify Archery" effect left over from when his customized gauntlets disappeared during a sloppy mod update (the original item's form id changed). Is there anyway to remove the effect without the item (I've dropped everything including quest items, the enchanted object's ghost effect is still there despite the object no-longer existing)?

did you try using console command to reduce your archery skill by the same amount?

Yes, wasn't entirely useful as it is a percentage which changes the amount everytime the skill goes up. I also tried removing it via modav marksmanmod (the actor value that governs it) and whilst the actual effect is gone it is still listed on the Active Effects page (which is annoying).

The only thing that has worked so far is the resurrect command (used on the player character). Though that is only half useful because all non-item effects are removed as well (including werewolf resist disease, sailor's repose, Ancient Knowledge etc). Only Agent of Mara, perk given effects (Greater Magic Resistance) and race effects (Nord - Resist Cold) reappear on save reload.