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How you suggested Deandra is how I am implementing it, I just didnt describe it well enough.

From in game it should look like this:

player uses Hunter's sight skill (VampireHuntersSight)
|
v
VampireHuntersSight modified to run script instead of skills
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v
HuntersSightScript checks for ability (AbHuntersSight) currently on the player
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-> If yes
-------Remove AbHuntersSight from player
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-> else
--------Add AbHuntersSight to player

end

AbHuntersSight is the actual skills while VampireHuntersSight is now just a script effect.

This "seems" to fail at the second statement because the Hunters sight DOES have a timer still and also has a visual effect that I removed.

It appears that the files I have edited are doing nothing or are being reverted/overwritten back to the default behavior. Other mods included are OOO/KTKhajiitNightEyeToggle/FixingFathis. Im really at a loss and this is driving me insane.