I started my thesis with different documents for the different sections and used Endnote with numeric references. Just now I realized that the references do not adjust themselves/merge when I merge the documents content. Is there anything I can do?
They should, unless you have them in sections and the sections are independently generating reference lists as defined by the output style settings. What if you change output styles and update? Do they combine then? If so – then return to your preferred format, and update. (this is in the document - it doesn’t affect how the document is formated if you just change the output style in the Endnote program itself).
If not – make a copy, then unformat (“convert to temporary citations” NOT TO PLAIN TEXT) the citations (assuming you have the library) and remove any residual reference lists, then update citations and bibliography.
If none of that works, then you should unformat the documents before joining them. Then update.