I managed to fix it. I was using the no tonnage limit mod, this was the issue. Uninstalled that and pilot issue is gone.

I think i would rather keep a tired commander then lose my salvage

So there are some work-arounds for PO.
I published in other posts.
Sometimes you have to swap out the commander with other pilots in bays but sometimes you can access the Barracks by clicking the current commander.
It is dependent on what mods you have, for some reason.
PO should be kept near the top, over the Advanced Careers Mod, but, under Under Tonnage Bonus mod and Updated Employment mods for best effect.

This is a common problem that is caused by having some other mod load after Pilot overhaul. Go into the mods folder, open the pilot overhaul mod.json file and set the number from 14 to 90 or something a bit higher. should solve your problem.

Not tonnage limits Load order is 99 by default, so Change pilot overhauls accordingly.

Or lower No tonnages.

The Commander's day has finally come.
https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=2950466866