I need to format references in a paper, which has a main text Word document, and a supplementary Word document.
To ensure that EndNote starts the reference list in the supplementary Word document after the last number in the main text (e.g. if numbers 1-53 are in the main text, and 54 onwards in the supplementary) I did the following: (this is to remind me for the future!)
(i) Turn off 'track changes' in the supplementary doc, and paste in the introduction+results+discussion+methods from the main text document at the top of the supplementary document.
(ii) Format the bibliography in the supplementary document using EndNote, and save a copy of the merged document that contains the EndNote field codes. This converts the EndNote reference numbers to plain text, so EndNote no longer recognises them as references.
(iii) Then select 'remove field codes' in EndNote to remove the EndNote field codes from the merged document, and save a copy of the merged document without the EndNote field codes.
(iv) In the main text document, turn off 'track changes', and paste back in the Introduction+Results+Discussion+Methods with the formatted references, from the merged document without the EndNote field codes. Then paste in the reference list from the merged document without the EndNote field codes.
Note: By turning off 'track changes' in the supplementary and main text files for this part, you ensure that the copy and paste of the large chunk of text isn't just tracked as one huge insertion, so earlier small edits you made using 'track changes' turned on should still be recorded.
Note 2: Remember if you submit the version of the main text without the EndNote field codes, and the journal then asks you to make some changes, you will need to go back to editing the version of the merged document that still has EndNote field codes (not the version of the main text that you submitted, that lacks EndNote field codes). (Learnt the hard way : )