How to ensure local library uploads to online account

Liz.mcgovern · 2026-07-13T21:29:24+00:00

I'm moving an Endnote library to Zotero. I am using the same Zotero login account on laptop A (where Endnote library is) and laptop B (which will become primary laptop) and have deselected auto-sync on both.

After many initial problems (which I figured out) I managed to export citations and files from Endnote groups and import them to Zotero (both on laptop A). After I dealt with merging the duplicates and deleting the trash, I synced the library and closed the package.

I opened an empty Zotero on laptop B and all was great, it automatically downloaded the whole library (with files, yay) - all was as it should be.

Today I looked for a reference in laptop B Zotero and noticed a collection/folder was missing. I closed laptop B and opened A, where the folder appeared to still be there - confusing as this was the library that went online and then onto laptop B!
I thought, ok I'll push the sync and it will upload to the cloud and bring the folder to the account but when I did, it started reducing the library and the folder I was looking for disappeared. It lost about 80 refs, but there were only maybe 20 in the folder in question.

All I want at this stage is to have the library that is on laptop B (even without the missing collection). I would like to understand what happened so I can avoid this in the future. I don't want the reduced library that is now in my account to replace the fuller one on laptop B.

Should I delete everything from the library on laptop A and sync it - so now the online a/c is empty and then sync laptop B? I'm hoping that everything locally will transfer to online, but afriad that could empty the library on laptop B.

I'd be very grateful for your explanation and some guidance. Thanks

dstillman · 2026-07-13T21:31:06+00:00

See Changes Not Syncing and provide the requested info if you're having trouble.

Do not delete anything.

If things disappear during sync, it means you deleted them somewhere else. There's no other way for that to happen.

Liz.mcgovern · 2026-07-15T07:48:15+00:00

Thanks for that link.
I ignored laptop A and added the missing folder manually on laptop B by drag and dropping a folder of pdf's. Then I did a sync on B after turning back on all settings for auto-sync including files etc. There are 1,281 items.

However, in the link above it provides a link to check the web library and it now displays 1175 items. I checked again today to see if it needed time to embed the change, but it is the same.
Why would there be a difference between them? What should I do?
Thanks

dstillman · 2026-07-15T12:11:22+00:00

We can’t help without the info requested on that page.

Liz.mcgovern · 2026-07-15T14:24:00+00:00

Thanks for your reply.
There were no errors displaying but I created an error report 2059680474
Is that the info requested you mean?

dstillman · 2026-07-15T14:55:17+00:00

That's not what's requested on that page. See the last step.

Liz.mcgovern · 2026-07-15T14:58:44+00:00

D982897406.

dstillman · 2026-07-15T14:59:34+00:00

And the rest of the info requested in that section?

dstillman · 2026-07-15T15:00:03+00:00

That debug output doesn't show you as having made any local changes since the last sync, so there's nothing to upload.

Liz.mcgovern · 2026-07-15T15:06:14+00:00

https://www.zotero.org/liz.mcgovern/library
Local library has 1281, web library has 1175
I cannot tell what is missing.

The steps are:
1. In the Help menu, go to Debug Output Logging and select Enable, or, to generate debug output from Zotero startup, select “Restart with Logging Enabled…”. (If you’re not able to access the Help menu, see Reporting Startup Errors instead.)

2. Immediately perform the relevant action (syncing, saving, importing, etc.) and reproduce the problem you’re experiencing.

**I did this, enabled debug output, synced the library. The web and local libraries are still not the same - which is reproducing the problem**

2. Before doing anything else, return to Help -> Debug Output Logging and click Submit Output, which will disable logging and submit the output to zotero.org. A window should pop up containing a Debug ID (e.g., “D12345678”). Click “Copy to Clipboard” and paste the Debug ID into your forum thread.

** I did this**

dstillman · 2026-07-15T15:07:16+00:00

6) Further troubleshooting

If you’re still having trouble, post to the Zotero Forums (in your existing thread, if you have one) with a Debug ID for the first sync after making a change that doesn’t sync (e.g., making a change to an item in the online library that doesn’t appear in Zotero, or vice versa), along with a description of what’s not transferring, including the zotero.org URL after selecting the item in the online library if it appears there. Start debug output logging before making the change and keep it going until the sync has ended.

Liz.mcgovern · 2026-07-15T15:35:09+00:00

I figured out that the items I had uploaded into the 'unfiled' collection were not recognised as items in the web version. Although this makes no sense, I moved them on the local library to a new collection with a different name and after syncing, both libraries are the same.

Why would the web library not see this pre-existing collection?

dstillman · 2026-07-15T15:39:26+00:00

You don't add things to Unfiled Items — it's just a virtual collection showing you items that aren't in any other collection. It's possible that some bug caused items not to be uploaded previously, and moving items to a collection would be a local change that would cause them to be uploaded now.

That's why the debugging process here requires you to provide debug output for making a local change that doesn't sync. It usually fixes the problem, and regardless, we can't debug sync problems that occurred in the past, only cases where you can capture yourself making a change and having it not sync.

Liz.mcgovern · 2026-07-15T15:50:48+00:00

Thanks for your responses.
I didn't know that about the 'unfiled' but of course it makes sense.
It is however strange that the local library recognised the addition to this collection (and allowed it) and counted the items - and the web version just didn't count them.

Perhaps the system should throw up an error message when this mistake is made?

dstillman · 2026-07-15T15:52:54+00:00

I mean, it's fine to drag items into Unfiled Items — it's just identical to dragging items into the library root, because all it's showing you is items not in a collection.

There's no "error message" to show here. If something doesn't sync up to the online library after you add it, that's obviously a bug, but as I say, we can't debug it unless you can capture it in debug logging.