So, I did a couple of flights yesterday. KPDX to KSAN and then PHOG. I left it on the ground at KSAN for about 90 minutes, with ground connections, but left the ELEC HYD pumps on (my bad). So, when I got back, I had two overheats. (Now, in real life, I would be fired and the flight delayed, but I carried on and per the QRH turned them both off and continued. So, while flying with the active failure, I had a freeze to CTD. When I reloaded, no failures. Do they automatically reset when you reload? Is that normal? Thanks.

This is a bummer. I guess you could always re-activate the failiure, but I think this leads to a bigger issue, does a CTD reset the counters in the SBF module? I think it is already a mistake that the NGX does not have the ability to scale the hours required to see service based failiures, and having the counters reset will only make it worse.

... having the counters reset will only make it worse.

A CTD does not reset the service based failure counters, so this is a non-issue.