I had this problem too and found a couple reasons for it
First, the intake for my filter inlet had plastic slits to keep things that are too big for it from going through, i found my axolotl stuck to it by the suction, once time he actualy got a gill stuck in and a small piece got ripped off
I had to put some filter media over it to keep that from happening
The other time i noticed it happening I had neglected my water changes for a couple of weeks
The water still looked clear and tested clean, similar to your, but his gills still seemed to whither and shrink over several days
I started doing bi-weekly (twice a week) water changes and his gill have grown back very nicely
check for anything the gills may be getting caught on, watch him while he is active and see if the axie gets caught on anything
How often do you change your water?