I have generally found it safe to read from my NTFS drives in Linux (I avoid writing if at all possible). This time, however, when I went to load the result of my work back in Linux, it could not read the folder (Thunar reported some generic IO error). Going back into Windows to investigate, Window's opinion was "It smells like Linux has been here! I can't STAND that guy or anything he touches, so I burned the folder just to be safe. You can thank me later."
As best I can tell, it had something to do with a combination of:
1. Windows Update needing to do things upon shutdown and startup, but then not booting back into it for a month.
2. Linux having been in hibernation rather than halted. Might have had some access bit set on the NTFS drive when it hibernated? I don't actually have the domain knowledge to claim that is what might happen, so it's a complete hunch.
This was really just a rant to get out the anger at lost work. This article was quite timely, and while I'm not glad to see people share my pain (because it's still pain in the end), I hope we one day see improvements.