Is this simply an effect of tabs?
Document 1, with bookmarks.
When the tab is open, you see the bookmarks and pages.
Document 2, no bookmarks
When the tab is open, you see no bookmarks.
Perhaps you actually want the tabs in separate windows (you can drag tabs out, or turn them off).
No idea. But in this case something else was afoot, and I should have reacted to it: when I quit Acrobat and reopened the PDF ALL bookmarked annotations had vanished (a days' worth of work)—which is the appearance I was getting in the second window (as if it knew what was really embedded in the document but the first window, which showed bookmarks, did not).
This is not the first time that Acrobat has stripped out bookmarks from a document for no reason. I don't know what causes it. In this case the problem went all the way down: when I looked for earlier versions (in SugarSync, which saves up to 5 at a time), all had been similarly stripped, which ought to be impossible since they were showing in the most recent version, and that version added a few more to ones that I had worked on successfully in the morning.
I typically do work in two modes: iPad (using PDF Expert) and a mac (docs synced by SugarSync). Too many moving parts to know which one is the culprit: Acrobat, the iPad app, or SugarSync. (At the time this occurred I was using Acrobat and the file was syncing to S-Sync. I just hope I will have the sense to save a file under a new name next time this happens and that way possibly avoid the corruption. Not sure that will work though.