Problems syncing between EndNote X6 and EndNote Web

I’m having problems getting my libraries to sync. The first time I tried it I got my EndNote Web groups appearing on X6 in the unfiled groups but no records in the groups. Nothing transferred to EndNote Web. The second time I tried nothing transferred at all, not even the groups. Can anyone shed light on what is going wrong?



I have had this problem in the past as well.

Are you using an Endnote library that you have used with previous versions of Endnote?

I found that when i created a new library with EndNote X6 the sync process to obtain references from EndNotweb worked without any problems.  I then imported the references from my old library into the new one and put them in a new group and the sync process worked in the opposite direction as well.  It showed all references and groups correctly.

Hope this works for you

After you attempt to Sync, look for the Sync Status option in the Groups pane on the left side of the library. If there are any “Sync Errors” listed, please contact Technical Support:

Jason Berman
Technical Sup Rep RS

Thomson Reuters

Phone: +1 800-336-4474

Thanks for your reply. Yes, the sync status is showing sync errors (Service. Reference store. Internal error) so this is probably the problem. I’ll contact Technical Services.


I am having the same problems.

But I was especially horrified because he wants to sync everything: he only send over empty groups.

I only used to transfer specific groups from Web to Desktop and vv.

I do not see that option anymore.

So for the time being I will keep my Endnote X5 alive.


We were having similar problems and creating a new library helped as did going to X6.0.1

I’ve just discovered something new about Groups and I’m keen to know if anyone else can explain this. Here is what I did:

  1.  First of all I synced my libraries then:
  2. Create a group in desktop EN – call it ‘desktop’ for example
  3. Add three references to it
  4. Create a group in EN web – call it ‘web’
  5. Add the same three references to it
  6. Press Sync
  7. The references that were in the desktop group are removed from the desktop group
  8. The web group appears in the desktop library under ‘unfiled’ with the three references intact
  9. If I then create a new group in desktop (with a different name) and the same three references are copied to that group
  10. Then the library is synced
  11. The group is transferred to web with the three references intact AND the references are intact in the desktop group


  1. Does this mean that references that appear in more than one location will always be removed from desktop groups when the libraries are synced? Or was it the order that I created the groups (ie. the web one was created last)?
  2. Why did I get a different result when I then copied the same references from one desktop group to new desktop group (with a different name) then synced the libraries again?

Is there a logic there? I’m at a loss as to how to explain this to our users…

Hi michelle_h,

Do you get the same results if you Sync in between steps 3 and 4?

I get the impression it has trouble dealing with a situation where the user has an existing EndNote Web library that’s very different from the Desktop one.

I teach EndNote Web to students who will be using it as their primary reference manager (because it’s free with our site license for Web of Knowledge) so my EndNote web library is fairly complicated and has a lot of groups and it’s been created independently of my EndNote Desktop library.

When I tried the effect of syncing. I found that the EndNote Web groups were copied down (but had no contents) while my EndNote desktop references were copied up into my unfiled references.

If I copy references in Desktop into one of the empty groups downloaded from Web they’re uploaded into that group.

I couldn’t get it to sync to download the uploaded references into an empty library on another computer which I would have expected to be the main reason why somone would want to use sync.

My guess is that it’s set up to be cautious about the way it handles libraries that are very different (which is probably a safety feature for most users).

Interesting: if I synced before creating a folder in web (with a different name but with the same references) the groups in both desktop and web remained intact after syncing. So my reading of this is that a sync should be done after each action to either desktop or web or is there something else going on that I’ve missed?

Thanks for your help,


Yes up until now staff and students have been able to use web and desktop as independent entities and only sync  what they wished. This change to how sync works represents a risk for people who are used to working this way in the past.

We are thinking of putting up a warning for users of previous versions of the desktop version because it is so easy to lose references when syncing. We have also had some problems with people trying to sync to new/empty desktop libraries. The revised video goes through the steps but I really fear that users will not do this. I didn’t find the steps very intuitive and I’m pretty sure I have more patience for this sort of thing than our students…

I agree with you about the cautious approach - it probably is related to that. I do wish there were more explicit warnings about group syncing though: on my first sync a whole bunch of references (luckily test ones) just disappeared from both desktop and web. A scary prospect for the serious researcher…

I guess part of the problem is that both Mendeley and Zotero do expect the user to create an empty library and sync when moving between computers rather than going through a complicated process to re-create the groups structure.

I suspected that the problem could have been that you’d been making changes to the same individual references, first on the web and then on the desktop, and when you chose to Sync afterwards only the more recent ‘change’ to an individual reference would take effect.

In general it is safe to make changes in the web and desktop and not sync. If the changes are to reference data and a sync didn’t occur in time for us to know exactly what changes were intended, we will create a group called “Sync Conflicts” and allow you to see a side by side view of what changed locally vs on the web. However, if reference metadata(read/unread, ratings, trash state, and group membership) is what changed on both the local and web, then it automatically chooses what changed last.


I can’t synchronize with endnote web too. Also, I am not able to do  articles search in the database. It looks like a problem connectin to the server. And I can’t find a way to change it. I had Endnote X6 but I decided to uninstall it and install it back again, in order to see if it would be enough to solve the problem. Now I have the X7 version and the problem is still there. Here is the window that shows when I click on the red sync error button on the left panel:

Sync Details
Sync was last run: Never
Sync Status: There are changes that need to be sent.
Error Code: Client.Error.Unknown
Error Message: EndNote “Sync” could not connect to EndNote Web.

Local Sync Library
Library Name: endnotelibrary.enl
Records: 0
Groups: 0
Attachments: 0

Online Sync Library
Serial Number: Unable to contact EndNote Web.
Records: Unknown
Groups: Unknown
Attachments: Unknown

Sync Limits
Number of Records: Unknown
Number of Groups: Unknown
Number of Attachments: Unknown

Can you help me?

Thank you very much