Not sure if this is a bug or it's intended; I was fighting a stack of Pirate fleets and lvl'd up between battles. I put pts in the tech tree which gave me a couple more OPs which I added to capacitance (only change I made). The next fight took place right after leaving the refit screen before the refit had time to finish. However instead of just missing the extra capacitance, I was missing all my hullmods (ITU, Frontal Shield emitter, Aux Thrusters, and many more!).
Admittedly this doesn't happen very often since that minor a refit takes less then a day to complete but thought you should know. Luckily I was piloting a paragon and it wasn't a big pirate fleet so I still won, just took longer