nope... the fact I have a HP option is a miracle at all
through a strange quirk of programming, if you leave the massive RU/CU option on, when you increase power to systems in the carrier, it will overheat instantly. It's best to turn the RU/CU option OFF after you have generated plenty of it, as that option may affect certain other unknown parts of the game at times.
we added a reset heat option, which will be posted shortly
we have no solution for one-off problem and unintended consequences of scripted battle sequences or scripts in the game that are based on unit HP, etc.
you will have to reload mission from scratch or replay previous mission and not use whatever option( s) may cause problems for specific mission events
for instance, some enemy ships if you set them to low HP using the HP options, they will never die because cut scenes are dependant on those units dropping to a certain HP, etc. you just have to deal with it individually. we aren't playing all 1000 or whatever missions and then trying every circumstance to see if some scripted thing is broken.
Also, note that the game has already patched at least once, which they are fixing internal bugs in the game that have nothing to do with the trainer.