Yes, everything was properly unmounted and no, there was no Windows boot in between. And no I am not using suspend or hibernate on the Linux or the Windows side either (fast boot and all that crap is also disabled; it’s one of the first things I do after installing Windows).
Also, said symptoms occurred live, right before my eyes. I.e. while Manjaro was running. I had ls’d (well, technically I use lsd but the readdir() call ought to be equivalent) the folder some minutes before, then suddenly as qbittorrent had finished its first downloads the files disappeared both in Dolphin and “from ls’ view” - in hindsight this only reinforces the notion about moving files being the culprit, btw.
I only rarely boot Windows these days, but I do it. Consequently I need a proper file (journaled) system to share between both. exFAT is not that file system and all Windows-side solutions for Linux file systems have been borderline unusable and very very fragile (to the extent that monthly security updates were able to break some of them).
PS: the comment by @omano from here resonates a lot with me:
I wouldn’t work on Linux file systems from Windows, and I would trust more the
NTFS3driver by a corporation that made working on file systems for almost 30 years its core business, than a driver rewritten from scratch on a GitHub project by one man. At the end of the day you do what you want but I don’t see how that makes more sense “the other way around”.
It reflects the position I held just until before I encountered those issues described above. But given even Linus Torvalds describes ntfs3 as still fairly solidly experimental, I think I’ll rather revert to ntfs-3g and live with the somewhat lower performance. Data integrity is also a performance trait to me. Search for (for the source of this quote):
Subject: Re: [GIT PULL] ntfs3: bugfixes for 6.0
Date: Wed, 17 Aug 2022 14:55:38 -0700
I am unable to include links in my replies, it seems.