I had a bunch of files open in 1.7.11. I set Reopen last open files at startup to "Always." I then updated to 1.7.15 and the file list under Window was blank. Now I have to re-load all of those files one by one. (Fortunately I have an Applescript which saves a list of all open files every hour.)
This is strange, as we always reload the last open file when updating the app with the updater, even when you don't normally do that. However, note that even when you don't reopen the files, you can always reopen the last open files from the Bookmarks menu using the Previous Setting menu item.
FWIW I have Skim at /Users/Shared/Apps/PDF_Viewers/Skim.app. I don't store in the default location /Applications because the backup service Backblaze does not back up that folder. That's all that I can think of that might cause this problem.
No, that should be irrelevant.
I really don't know what went wrong here. I don't even now where it went wrong (at launch or at terminate when saving the open files?) And it is not possible to find that out now, it is too late. It normally works as it should, so it is not a systemic problem. I have no way to further investigate this and find out, so there is really nothing I can do.