"Update citations and Bibliography" in Word: it takes to much in long documents

Heavens no.  You are just returning endnote formatted fields to their convert first to temporary format, and then cleaning up the document by “convert to plain text” to remove any random garbage, and then updating to reformatting the curly bracketed endnote citations back to the formatted version (according to the output style).  If there is was corrupted field, it might need to be reinserted.  

Sometimes, just converting to temp and reformating does the trick. 

ALWAYS make a copy before doing these steps so it it all goes pear shaped, you still have the origninal.