Endnote has started references from 1 again in my document.

Not easily.

Do you have a previous copy, which you can convert to unformated citations and compare to the plain text version?  Accept/reject (which ever is appropriate) keeping the citations in curly brackets and the opposite to keep the edits you want to keep.  Any newer citations left, will need to be reentered.

There are other ways to work thru the citations – for example, if numbered, you can create a new library numbered the same order by dragging and them dropping them and convert the numbers to {#number} by searching and replacing the ( with {# and ) with } and ask endnote to update the citations, with only  the new library open.  – if there are groups of references, it might be easier to just bite the bullet and replace them all.  If you are using an author, year style this is sometimes easier.