LR might of made a minor change to the file when re-imported.
But you have changed it in PS.
I don't understand what you mean by "re-imported." Just to be clear, the sequence is:
1. Create new PS document and Save As foo.psd
2. Import into LR (the only reason for importing is to add foo.psd to the catalog).
3. In LR -> Photo -> Edit in... -> Adobe Photoshop CC 2015 and select "Edit a copy"
LR creates foo-2.psd (this is "the disk copy") and sends it to PS for editing.
4. Make changes to foo-2.psd in PS
5. File -> Save (this is where I get the warning dialog)
The file is never "re-imported." It doesn't have to be, because when you Edit in PS from LR, LR knows that the file is being edited, and automatically updates the catalog when you save it There's never any need to re-import the file or Synchronize folder.
Obviously the disk copy changes when PS saves, but the warning says the file was changed since PS last opened it.
Right, not Re-import as LR already has foo-2 in the catalog. PS is giving you that warning because the file is already on the disk and you have now made changes to it.
But the normal behavior of File -> Save in any Windows program is to quietly update the file, and PS is no exception. If I had used File -> Save as... I would expect the warning. The warning tells me that something else (not PS) changed the file.
Aha! In this discussion from 2012 (and others like it), users reporting the same problem were told "something else must be touching the file." Since my problem started yesterday, I thought about what might have changed on my system. Drum roll please...
I re-installed Bridge CC (2015).
As a Lightroom user, I almost never use Bridge, although I have it installed. Yesterday I needed Bridge for something. I tried to launch it, but it would not launch. So I uninstalled and re-installed it from the Creative Cloud desktop app and everything was OK...
But that's when I began getting the "disk copy changed" warnings for nearly every save from Photoshop.
Note that I get these message when Bridge is not running, only Photoshop and Lightroom.
I will uninstall Bridge and see if this eliminates the bogus warnings. Meanwhile, I'll post to the Bridge forum and find out if anyone else has had this problem.
Since uninstalling Bridge I have not gotten a single bogus File -> Save warning from Photoshop.
I'm marking this as the correct answer. If I get even one File -> Save warning, I promise to un-mark it.