I have a setup with both OSes on an SSD and a brand-new HDD with a FAT32 partition so it can be easily accessed from both Ubuntu and Windows 11.
For some reason, files created on Ubuntu aren't visible on Windows 11 and are silently overwritten if I do any disk operations on Windows (here demonstrated by taking a screenshot and saving it to the drive). I lost a whole day's worth of work by doing it on Ubuntu then moving some big files into my HDD on windows.
I have no idea what's causing it, but it seems to consistently happen exclusively when I write on the disk from Windows 11. I want to be sure it's not a problem with my HDD (since it'd been working well enough when using it exclusively on Ubuntu).
HDD seen from Ubuntu, showing a test file
HDD seen from Windows, not showing the file
HDD seen from Ubuntu again after
Reformatting the disk to use a GPT table and exFAT partitions did not solve the problem. Interestingly, Windows 11 didn't even notice the disk had been formatted or changed until I manually went to the partition manager and refreshed it.
As described in the comments, disabling Fast Startup seems to solve the problem.
Thanks to the similar questions feature, the editor has shown me this question in this very forum, which I hadn't found with the search feature. The situation is slightly different, since my problem is happening in a completely different drive, rather than between partitions, plus it's Windows 11.
I've posted an answer there, detailing my observations and the solution suggested in this question's comments.
Please refer to this question for a solution.