This doesn't just happen on its own, so most likely you either deleted the items accidentally or reverted to an older version of your database when you weren't fully in sync with the server. If you toggle field codes in a document and provide some URIs for example items (e.g., http:// zotero.org/users/3279/items/ABCD2345), we can tell you if they were ever in your account online.

Do you have any backups of your Zotero data directory?

@danstillman:

I suppose database reversion is probably the answer.

Here are two URIs from a current document.
One is an old citation (2008?), the other recent (2016):
http://zotero.org/users/3279/items/UVEA8WCK
http://zotero.org/users/3279/items/ES4HT5TK

I did not realize that the data directory needed backing up.
I thought that a paid subscription for server space was enough insurance.

@DWL-SDCA:
Standalone only. FF not installed.

(For what it's worth, if you did stop uploading due to an upload error, we're going to add a more prominent warning in an upcoming version to better warn people when syncs aren't going through, since it's possible to overlook the current sync error icon.)

I didn't "switch" computers, but I did install and use Zotero on another machine in July/August. Could this be the problem? And if so, is it possible that my old citations exist on that machine?

Oh, well, certainly. Isn't it possible then that you just created items on that computer, and cited them, without setting up syncing? So then if you still have the documents but are now using your original computer, you wouldn't have those items. You'd need to sync that computer (after making a backup of its data directory for good measure, but no reason they should be affected by a sync).

I'm guessing that's the extent of the issue, but just to address the other points:

ES4HT5TK was recreated after losing it once.

Right, that's not relevant then. I'm just looking at the item keys, so a recreated item has no relation to the old one.

UVEA8WCK had to have been on the server at some point, since I've synced my directory more than once in the past eight years.

It hasn't been there since 2010. But as I say, it was created long ago enough that it's not worth worrying about this one.

As for the zotero.sqlite, I checked the local directory and it's up to date (latest is 10 minutes ago).

Well it'd definitely be up to date, since it's your active data directory. The question is whether you at some point had Zotero set to a different data directory and the setting was somehow lost (e.g., a custom directory, or if you initially used Zotero for Firefox, Standalone was using that directory, and then you uninstalled Firefox, causing Standalone to revert back to the data directory in its own profile directory).

The most important thing to do is to check whether the 'storage' directory in that one has folders from between July and November. If not, and you didn't delete them in Zotero, they were never there. (Zotero doesn't delete storage folders separately from items.) So if those don't exist, you should look for another data directory, either on this computer or another one.

There was and is no sync error indicator.

Yeah, actually an upload error would almost always be logged server-side too. So more likely that auto-sync wasn't enabled or, if this was the other computer, syncing just wasn't set up.

(I know you've used MLZ/Juris-M in the past. Not sure if you've used that anytime recently, but obviously we can't speak to what that might do with profile and data directories.)

I have TimeMachine backups of my entire drive. But wouldn't restoring my zotero.sqlite from one of these potentially wipe out everything I've done since then? Or would the items on the server but not local then sync with my local profile?

If you found a backup with the missing data (which you could tell without restoring by looking in the 'storage' directory from the backup) you'd be able to combine it with more recent data. Generally speaking, you'd just need to make sure you were fully synced, make a backup of your current data directory, replace it with the backup, and then sync, which would pull down the recent data and upload the data from the missing months.

If the missing data is on another computer, you'd just need to sync it.

I recently had the problem that entries disappeared while the pdf was somehow still somewhere.

Could you say more? What does "somewhere" mean? Again, items just disappearing isn't really something that happens — it's more likely that, as was the case above, you're using a different data directory than you were previously, and items hadn't fully synced before. But you'd have to explain the PDF part.