I'm having a similar issue, where I'm syncing my TaskPaper files via Dropbox and also editing them in iOS. When I update a file through iOS, the next time I launch TaskPaper on my Mac the edited file will fail to re-open. I do have the System Preferences "Close windows when quitting an app" properly unchecked, and any other unchanged TaskPaper files do restore properly.
- Mac OS X 10.11.4 (though this has been an issue for me at least back to 10.11.0)
- TaskPaper 3.0.1 via Mac App Store (though I had the same issue when running TP2 from the MAS)
- Dropbox 3.16.1 (though earlier versions were also affected)
(Pure conjecture beyond this point; I know just enough about Mac internals to get things maybe half-right) It's like the Dropbox sync is replacing my todo list with a new file that has a new file ID, and TaskPaper(/Mac OS X?) tries to reopen the list using its (now dead) old file ID--and then doesn't fall back to the file path, when that fails.
I've tried searching around for anything that might explain this, but finding issues about restoring previously opened files synced via Dropbox is... difficult. I wonder if this affects more than just TaskPaper, though TP is by far where it's irritating me the most.
(Thanks for the excellent application, Jesse; I've been happily using it for years now!)