Thanks for the helpful comments. I have good news to report. A merge sync at work seems to have fixed the problem. My notes are back where they should be, and the changes I made at home were entirely preserved. Phew. Here's the weird thing: Upon syncing, the merge window produced only five conflicts, none of them having to do with my notes. In fact, none of the conflicts were patently conflicting, which is to say that every piece of data displayed as "local" vs. "server" (including time stamps), which I was then asked to resolve manually, actually matched already. So something is going on there beyond my field of vision. As for the notes, they seemed to work themselves out, as if by magic.

I appreciate the logic that this problem had something to do with versions b6 and b6.1, which were out for a short time. But I'm not entirely convinced -- because when I got home I made it a point to upgrade to b6.2 before syncing. In fact, Firefox practically made me do it by presenting the option on startup. So... someone might want to take another look at 6.2 and make sure the issue is fully resolved.

For others who might encounter this problem, I highly recommend backing up your library before trying a merge sync, since merging is still very much in development. For what it's worth, I think it's a great tool to have. At the very least users benefit from the increasingly clearer distinctions among various types of syncing -- they are not created equal! -- including the default sync.

Initially I wasn't sure whether, in a default sync, certain local changes would be privileged when compared with the server version. That's what I think most users would expect; otherwise, they might see some unusual behavior -- for example, a reference removed from a collection, but not the library, might unexpectedly reappear in that collection following a sync. (Fortunately, this is not the case by default.) The mere availability of merge syncing has helped make this distinction clearer, but some related documentation would also help.

Thanks again, and good advice. For the record, I had already upgraded to b6.2 at work, then synced by "restore to server" before going home and encountering the problem. So I'm still not convinced it has (solely) to do with a bug (solely) in the older version.

But thanks for explaining more of the syncing nitty-gritty there. I'm not sure we're talking about exactly the same thing. Let me be more clear. Say I'm working on one local copy of my library. I copy a link from one collection to another, then I remove the link from the original collection. (In effect, I've just moved without copying from one collection to the next.) Then I sync again -- a standard sync, using the sync icon in the upper right -- or, say, one that happens automatically because I've enabled auto-sync. To my knowledge, the link I moved is not restored to the original collection, where I had just removed it. And that's precisely the behavior one would want, right?

On the other hand, I agree that if I leave this local copy running, then make changes from a different location that somehow contradict previous changes, then Zotero should "err on the side of more data." I'm guessing, but not sure, that that's what we're saying.

Excellent discussion. Might be useful to add that or something like it to the wiki, maybe on a page like "more details about syncing" or something. Many thanks.