I converted my research paper to plain text before submitting it to a journal, but added citations manually later on. Is there a way I Endnote can automatically detect the references that were added later, and create a new non-plain text file with the updated citations?
nope. your best bet is to compare the plain text version to an older endnote version (best if you “unformat to temporary citations” making it an endnote friendly version of the document but without all the “field crap” and then carefully accept and reject changes keeping the endnoted citations.