I use a mod that shows bright red all the time when you run out of supplies, plus if that would really happen, one cannot
miss it really - game will keep opening in the middle of the screen a "Accident Report" every few days - tested :)
I loaded my old save, then I did a test w/o any supplies and with low crew - the fleet was fine for more than 4 months.
I didn't fight with anyone during the run while "strange reset" happened, and I did not play around hazardous environments.
The only unusual thing I remember doing at the time was playing with Contacts in the "Intel" tab.
Not sure if I missed it, was added recently or is this from a mod, but I just only discovered there was a "call" button.
I did try playing with that button again (e.g. to see if I can deliver rescued people by the phone :) w/o visiting the planet),
but it did not trigger the reset.
If that was a quest/mission by any chance (I try to not skip any story and read all texts) then it would be too punishing
(loosing all ships and cargo), and there are probably a lot people skipping the text. So it more seems like some ugly bug.
I just wish I knew how to reproduce it.
And here is the enabled mod list:
Spoiler
Audio Plus: 1.1.3
Autosave: 1.1c
CaptainsLog: 0.1.6
Combat Chatter: 1.12
Combat Radar: 3.0
Console Commands: 2021.12.25
DetailedCombatResults: 5.2.2
Dynamic Tariffs: 1.4
fleethistory: 1.0.8
FleetTester: 1.0
Flux Reticle: 1.2.1
GraphicsLib: 1.6.1
Hostile Intercept: 1.3.2
Interesting Portraits Pack: 1.2
LazyLib: 2.7b
Leading Pip: 1.9.1
Logistics Notifications: 1.4.4
MagicLib: 0.42.1
Ship Direction Marker: 1.3.1
SpeedUp: 0.7.2
stelnet: 2.6.1
UnpackBlueprints: 1.1
Version Checker: 2.0b
Weapon Arcs: 1.7.0