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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.

Mel O.
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    The File000 folder indicates there have been file system problems on the drive, into which chkdsk has tidily swept the crumbs, & from where you can discard them at leisure. Make sure the drive is stable first. – Tetsujin Sep 29 '22 at 13:10
  • The drive is perfectly stable when accessed exclusively from Ubuntu. The only problems I've had so far were on Windows 11. I ran chkdsk manually to assess the situation. – Mel O. Sep 29 '22 at 13:21
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    Are you using hibernation on either system or Fast Startup on Windows? – Daniel B Sep 29 '22 at 13:22
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    Did you make sure it wasn't chkdsk that removed the files? Chkdsk doesn't give a damn about your files, its job is to fix the file system, for which it will sacrifice anything & everything without hesitation. – Tetsujin Sep 29 '22 at 13:24
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    Have you disabled fast startup in Windows? If another question is the solution to your question then we would prefer to mark it as a duplicate than copy the answer here again. [How to Turn Fast Startup On or Off in Windows 11](https://www.makeuseof.com/windows-11-turn-on-or-off-fast-startup/) – Mokubai Sep 29 '22 at 13:24
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    It's straight out of the box, no settings changed. I *thought* I was shutting Windows 11 down, but it appears it's got some kind of "hybrid" shutdown enabled by default. I'll try and turn it off (if I can find that setting anywhere). ( @Mokubai has sent a link above. I'll try that.) – Mel O. Sep 29 '22 at 13:24
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    @Mokubai Disabling fast boot seems to have worked (from a simple test using a single file). I'll transfer my backups back into the drive to truly put it to test. If marking it as a duplicate is the preferred option, then that's probably the way to go. I'll add an answer with a bit more detail and mentioning it happening on Win11 w/ exFAT and different drives, too. – Mel O. Sep 29 '22 at 13:39
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    When dual-booting with any Windows 8.x or newer, disabling its Fast Startup feature is a MUST. – ChanganAuto Sep 29 '22 at 13:56
  • Only badly-behaved firmware allows booting a different system rather than the hibernated one, by the way. But then, firmware is generally rather low-quality. // The comment above is part of the duplicate vote. – Daniel B Sep 29 '22 at 14:24
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    I don't consider that "bad" behaviour. It gives me more control over the computer (choosing which partition it boots from and how it'll boot). What's unequivocally bad IMO is hibernating the system whilst telling the user it's shutting down, as Windows 11 does. – Mel O. Sep 29 '22 at 14:51
  • @Daniel B, the lower level should not know what the upper level does. There is only one exception from the rule I am aware of. Your intended behaviour would require an information flow from the operating system to the firmware, like from the operating system passing TRIM information to a SSD. – r2d3 Sep 30 '22 at 12:21
  • [“The firmware notification is done by writing to the sleep-type registers with values that were provided in the S4 object as defined in ACPI 4, Section 4.5, Table 4-13, and Section 7.3.4. This indicates to the firmware that on next power-on, a resume will be attempted rather than a full boot.”](https://learn.microsoft.com/en-us/windows-hardware/test/weg/delivering-a-great-startup-and-shutdown-experience) – Daniel B Sep 30 '22 at 13:02

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