This is not in dispute and something that is easy to prove by getting into a fight with ATR:
Source: https://youtu.be/PL9Jtpp4FzQ?t=375
Yep, persistence from instance to instance is very iffy. From experiments, I do think it's intended that they retain the state they were previously in, but it often doesn't work, which suggests it is a bug.
An example of when it does work:
Source: https://www.youtube.com/watch?v=d286irXwmX8
NPC Anaconda clearly retained the damage I had dealt to it, while the FDL didn't immediately reenter SC.
They shouldn't care. CMDR's don't because in the current state of the game heat cannot hurt them. It's why half the CMDRs I've run into in hostile circumstances in the last year were thermal conduit boats...they know that they can last through a 20 minute fight being at 160% heat for half the fight with minimal consequences.
Even when heat based attacks were a threat, NPCs still didn't care, because they are there as flying pinatas...fodder for CMDRs to shoot down, and they have extremely poor self-preservation behavior, even if they do occasionally run.
That was a good one, and one of the few that made them more threatening, but yeah, clearly a bug and one that was quickly corrected.