Having this same issue. Positive skill XP levels, won't save skill upgrades.
edit: here's how I fixed it - I set my skill level down extremely low but kept the XP at the same high level - as soon as I gained a single point of XP it went back up to the proper value and allowed me to add and keep the perks. Haven't tested this solution for engineering, though!
[Edited by modpud, 3/30/2020 11:21:15 PM]
Okay that's working
this option may not toggle on until some peice of gear takes damage, like the shield. Wait to see the shield bar (for instance) go down when it's hit, then toggle it on.