I ended up giving up on native tools and msys2 entirely in favor of WSL2 after several months.
And then finally asking for a Mac after several more.
There are way too many bugs and quirks in every layer of this stuff, from missing features in the 'native' OpenSSH port by Microsoft to data loss bugs (!) in WSL2.
Mind going into this in more detail?
But they make it really hard to rely on. From random shutdowns, GPU unreliability to data corruption and performance differences with just using Linux directly, I had to move away from it and back to Linux because I felt like I slowly losing my mind troubleshooting these issues.
Latest issue was that the virtual disk file continued to grow beyond 500GB large while Linux still reported that it was just 20% full from the inside. So, reading about things, I gave optimize-vhd a try and boom, full disk file was corrupted.
So, gave it a try, hit a bunch of issues, left and not planning to touch it again until WSL3, and I'll be much more cautious then.
The issue seemed to be that sometimes files which the guest believed were written to disk were not actually written to the VHD file backing it, or the VHD file's changes were not actually written back to the physical disk. So sometimes upon a reboot (or after `wsl --shutdown`, which doesn't attempt safe shutdown IIRC), I'd lose files.
Generally it was only system files, and was recoverable by mounting the VHD for the guest to a new guest and repairing the OS in the worst cases, but sometimes did render the guest unbootable.
When I Googled the issue, I found people reporting similar problems on GitHub and Reddit going back years. On bare metal, the same distro I was running features atomic upgrades (on all filesystems), has survived power outages during system upgrades, etc.