Neck pickup losing output on LP studio?

I have a 2011 Les Paul studio with the original 490/498t pickups. A day ago, I took the pickup covers off, cleaned up the wax and reinstalled them coverless. I made no altercation s to the control cavity. Upon retuning the guitar the neck pickup is literally 1/3 volume of the bridge (which was unaffected by removing the cover). It's not a bad tone (kindve strat-ty) but it's extremely thin and lacking in girth. I cannot imagine removing the pickup cover resulted in this, but was wondering if I may have held the soldering iron on the back of the pickup too long to desolder the cover? Other than this I am clueless and frustrated. The guitar has the quick connect system. Everything else is working as it should...did I possibly fry the neck pickup?

did you change (lower) the pickup height when you reinstalled it ? ..if so, crank it back up closer to the strings.

Measure the DCR. The 490/498 should ohm out at approx 8ko and 14.5ko. You needn't remove them. Measure at the end of the cord. Flip the pickup selector switch to select the pickips. Maybe you used too much heat and created a partial coil short