I applied a few shield upgrades which permanently increased shield HP. One or two were crystals, and another was one of those algorithm cubes.
Then I bought a crystal at a station, which my advanced analyzer couldn't decode. I decided to try it out. It was a reflect positron beams or something, which is temporary. It removed all my previous permanent upgrades, and then the positron reflect wore off.
I am not sure if this is intentional behavior, but it seems odd that a temporary buff would cancel out permanent buffs.
Generally items can only have one enhancement (not counting buffs from other installed devices). The code that decides what to do when attempting to add an enhancement to an already enhanced item is old and complicated (IIRC). But it might be better to make field crystals that apply a temporary enhancement have no effect on already enhanced shields.
Fixed in 1.9 Alpha 2. Temporary upgrades do not remove permanent ones.