Since no one else has come up with any (easier?) approaches yet, the following *should* work.
Work on a copy of your Endnote-formatted document (preserve the original). First click the menu option to convert your copy document's Endnote citations to plain text 'unformatted' (in the Endnote menu within your word processor), eg {Smith, 2014 #1029}. If you're not familiar with that Endnote option, here's one library's simple guide to finding the menu option. https://libguides.adelaide.edu.au/c.php?g=874062&p=6275545
Now, you *could* just go through and replace each plain text citation by inserting the corresponding new Zotero citation one by one in the usual way ... and you're done. Depending on how long your document is, the following *might* be less tedious. ;)
Zotero can itself use unformatted citations, but not with the Endnote # item number included (Zotero unfortunately has no item number). eg for Zotero to recognize it, the above example would have to appear as {Smith, 2014}.
So you would first need to edit out all of those # numbers. That can be done manually, or a little less tediously with a series of Search & Replace operations to remove arbitrary numbers (while preserving the year), like this in MS Word ....
1. First search/replace all # with xxxx 2. Under More in the lower half of the Search/Replace dialog box, set Use Wildcards to ON. 3. Now search/replace the following string with nothing .... xxxx[0-9]{1,} (NB there should be leading space before xxxx; [0-9] replaces digits between 0 and 9; {1,} does that for strings of 1 digit or more)
All your citations should now be shown as Zotero unformatted citations, eg {Smith, 2014}. Then save the file to RTF format.
Finally, use Zotero's RTF scan facility to match those unformatted citations to those now in your Zotero library ... https://www.zotero.org/support/rtf_scan
RTF Scan wouldn't help here. It doesn't create a document with active Zotero citations — it just generates a final document with formatted citations and references. @jkaedtl already has that by virtue of having a document with EndNote citations.
A similar process with the ODF-Scan plugin might work, though, since that actually generates active Zotero citations.
There's no way built-in way to do this. Zotero can automatically relink Mendeley Desktop citations, but not EndNote citations.
Oh OK, I was pretty sure that there was a way to get to active Zotero citations ... so that must be with the ODF-Scan plugin mentioned at the end of the RTF Scan page. Which would require LibreOffice for that final stage of the process.
Parenthetically, I have mentioned before how I always used to write with Endnote using unformatted citations - with my Endnote library open on one monitor and MS Word on the other. If I couldn't remember an author's name when typing an unformatted plain text reference, I could just look it up. That meant I completely avoided the need to use Endnote's Word plugin until final document prep ... when the unformatted citations were translated by Endnote's plugin into active field citations, and the bibliography was then generated.
I understand that active/formatted Zotero citations can get slow on some platforms/large documents. So one thing that would presumably help with that (along with the OP's problem) would be if Zotero's Word plugins had the inbuilt ability to translate unformatted citations into active ones; which would only be needed at the end of the writing cycle. That might make Zotero less subject to the whims of word processors. ;)
To speed up inserting citations in large documents, you can disable automatic citation updating from the Document Preferences window in the Zotero tab in Word.
Endnote’s publisher has in the past filed capricious lawsuits against Zotero when Zotero used to have some interoperability with Endnote, so I would estimate there is zero chance Zotero will ever be able to work with Endnote citations in a document
Upgrade Storage
Work on a copy of your Endnote-formatted document (preserve the original). First click the menu option to convert your copy document's Endnote citations to plain text 'unformatted' (in the Endnote menu within your word processor), eg {Smith, 2014 #1029}.
If you're not familiar with that Endnote option, here's one library's simple guide to finding the menu option.
https://libguides.adelaide.edu.au/c.php?g=874062&p=6275545
Now, you *could* just go through and replace each plain text citation by inserting the corresponding new Zotero citation one by one in the usual way ... and you're done. Depending on how long your document is, the following *might* be less tedious. ;)
Zotero can itself use unformatted citations, but not with the Endnote # item number included (Zotero unfortunately has no item number). eg for Zotero to recognize it, the above example would have to appear as {Smith, 2014}.
So you would first need to edit out all of those # numbers. That can be done manually, or a little less tediously with a series of Search & Replace operations to remove arbitrary numbers (while preserving the year), like this in MS Word ....
1. First search/replace all # with xxxx
2. Under More in the lower half of the Search/Replace dialog box, set Use Wildcards to ON.
3. Now search/replace the following string with nothing ....
xxxx[0-9]{1,}
(NB there should be leading space before xxxx; [0-9] replaces digits between 0 and 9; {1,} does that for strings of 1 digit or more)
All your citations should now be shown as Zotero unformatted citations, eg {Smith, 2014}. Then save the file to RTF format.
Finally, use Zotero's RTF scan facility to match those unformatted citations to those now in your Zotero library ...
https://www.zotero.org/support/rtf_scan
A similar process with the ODF-Scan plugin might work, though, since that actually generates active Zotero citations.
There's no way built-in way to do this. Zotero can automatically relink Mendeley Desktop citations, but not EndNote citations.
Parenthetically, I have mentioned before how I always used to write with Endnote using unformatted citations - with my Endnote library open on one monitor and MS Word on the other. If I couldn't remember an author's name when typing an unformatted plain text reference, I could just look it up. That meant I completely avoided the need to use Endnote's Word plugin until final document prep ... when the unformatted citations were translated by Endnote's plugin into active field citations, and the bibliography was then generated.
I understand that active/formatted Zotero citations can get slow on some platforms/large documents. So one thing that would presumably help with that (along with the OP's problem) would be if Zotero's Word plugins had the inbuilt ability to translate unformatted citations into active ones; which would only be needed at the end of the writing cycle. That might make Zotero less subject to the whims of word processors. ;)
Endnote’s publisher has in the past filed capricious lawsuits against Zotero when Zotero used to have some interoperability with Endnote, so I would estimate there is zero chance Zotero will ever be able to work with Endnote citations in a document