This is an incorrect statement. There are plenty of changes in the configuration, including major compass changes and thrust-related changes including:
ATC_THR_MIX_MAN: 0.5 => 0.1
MOT_THST_HOVER: 0.2087 => 0.1250
PSC_ACCZ_I: 0.25 => 0.3
PSC_ACCZ_P: 0.125 => 0.2
My first blind guess was the all-up-weight change (a different battery maybe). When a copter is tuned tight for a particular weight, and then the weight drops, the old PID gains may become too high for the new physical layout, which can easily result in overheating. But in this case the battery current usually changes, and here it was about the same for the first and the second log.
The tuning is, by my standards, very sloppy, especially in yaw. If one compares, in both flights, actual versus desired pitch, roll, and yaw from ATT records, deviations in pitch and roll reach up to 2 degrees, and yaw deviates by 5 degrees easily, and by more than 10 degrees in the beginning of the flights. This is consistent with small rate PIDs in pitch and roll (0.06), default angle P values and recommended initial angular accelerations, which overall indicates lack of tuning: we are just in the “basically flyable” state, not in anything looking good. This cannot fly well, but - returning to the topic of the post - there is nothing in the tuning that would cause overheating.
Looking at other sources of information, I noticed that in the first log the reported onboard temperatures were in the range of 31-39 degrees C, where 31 is likely the outdoors temperature as it was reached in flight. The second log features 44-48 degrees. Unless there is something in the physical layout of the craft, you just hit a very hot day.
I have not got the particular nature of the crash that ended the second flight, but all the motor outputs spiked high and the altitude dropped. [Whatever happened, 60+ deg of motor temp might have also been the result of this short current burst too.] - as indicated below, current dropped here, so it’s not the reason for 60+ on motors. It may be that on the colder day the motors were just colder and you were not triggered.