Issues with lost and reorganised references when compiling a single word doc from many (Endnote X.0.2)

Hi all,

Im hoping someone that can help me with my problem of compiling several word documents into one, referencing from a single endnote library.

Ill provide as much info as I can, apologies if it is deemed overkill.

I am using Endnote verision X.0.2

I have 8 separate word documents (version: Word 2003), all independant of each other, however, the endnote library used for all 8 is the same one.

I am using the “aerosol science tech” output style, e.g. (obrien et al 2009)

When inserting a reference, I have my endnote library open, highlight the reference(s) and go back to the word document and insert the references using the endnote tab at the bottom of my screen.


I am currently trying to compile my thesis into one single word document from these 8 separate word documents and when I do (in the compilation document)…

  1. Some of the refereces are changed around and placed in the incorrect position automatically.
  2. Some of the references are removed from the compiled document (but are still in the library)

When compiling the 8 documents into 1 single document, I have both the final version open, and the relevant document open (one document at a time).

I highlight the text (including inserted references) to be copied, right click and copy, and move to the final version, where I right click and paste in the text + references.

Once this happens, Endnote pops up a screen that reviews anything between “( )” style brackets and to my frustration (even though I hit “ignore all” still replaces some of the items between “( )” with a reference that I never highlighted, for example, if I have a figure legend explaining what was on the (right) of the figure, it inserts a reference instead of “(right)”.

Should I have the endnote library open when I copy and paste the text and referenes into the larger document?

When I open “format bibliography” the box says that my temporary citation delimiters are left " ( " and right " ) "

If I changed those, would that stop the automatic scanning of the document for anything in “( )” brackets? If memory serves, before the missing and replaced references began to happen, I did change these toleft “{” and right “}”.

Ive since changed them back to “(” and “)”.

When I look at the instant formatting tab, I cant tell if it is enabled or disabled. It does give me the option to disable, but what will that do? The settings selected for that option are…

Scan for temporary citations

Check for citation changes

Again, should I deselect the “scan for temporary citations” option.

(Im not even sure what temporary citations actually are!!!??)

Ive been using endnote for a while now, without any issues, but Ive never had to compile word documents before. Needless to say of course, when I did need to, it happens to be a week before my submission date!!

Thanks in advance for any and all help, it is sincerely appreciated indeed!

A quick question: Do you need to have bibliography for each chapter, or do you need one big bibliography at the end of the thesis?

One suggestion: Stick with curly bracket { } for temporary citation. Using regular parenthesis ( ) for temporary citation will confuse Endnote if your text contains some ( and ) here and there.

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Thanks !

No, I only need a single bibliography at the end, and not for each section/chapter.

re: the { }, Ill give that a go again. It makes sence alright, that it would avoid any confusion with any ( ) used in the text, but I think thats where one of my problems started!

Ill give it a go again!

While I know you’re online…

Any ideas on why my referenes are disappearing and rearranging?

Much appreciated.

Can’t tell exactly why they are gone or rearranging, but I guess because the regular ( and ) were used for delimiters. Here’s what I suggest.

  1. Change the Endnote preference of temporary citation delimiter to curly brackets.

2. Scan through your individual chapter files, and make sure they are all at the right place.

  1. Back up these individual chapter files. Make duplicate for each, and work with the duplicate from this point and on.

  2. Unformat the individual chapter files (once again, do this with the duplicate). Now you’ll see where are the “Temporary citations” are located, and they are all enclosed between curly brackets. 

  3. Combine chapters, and make the master file. Make sure these temporary citations are still in place.

  4. Reformat your master file.

This should work.

1 Like


Ill certainly give that a go.

Ill report back later today with a report on how it went.

Sincerely appreciated indeed Myoshigi.

Looks like that sorted the problem for me.

Fantastic, thank you very much.

I have discovered what is happenng here… the reference link is not updating to the correct reference number…  So for me I am seeing ENREF_208 which wants to point toward a reference by “Smith” - but 208 is a reference by “Jones”…

I just checked to make sure the correct reference was in the list - and deleted the failed reference link.