Writing in case someone stumbles upon this like I just did.
I had this problem as well, and found a solution.
My docker was getting way oversized, which led to crashes.
Turns out that for some reason my NZBGet container lost its path to the data folder.
First I checked the container sizes and saw that nzbget was way too big (should be ~130MB).
I just went in on that containers settings and fixed the path.
After a restart everything working great again.
Now it could be that I forgot to fill it in, but I am most certain that I did fill it in and that it got lost during some reboot.
Some other settings got changed during the same time (my array auto-start on startup stopped. my containers that I selected to auto-start also stopped doing so).
Not sure what can cause settings to disappear like this, but at least the fix was easy.