Does it sound like it’s the problem described here — https://discussion.evernote.com/topic/24557-import-old-notebooks-into-evernote-using-enex-loses-all-note-links/ ?
If so, that’s the longstanding problem I refer to to. (that forum thread is from 2012). Given how long it’s been around, I’m not very worried that Evernote are going to fix it.
In theory, you could write a script that takes a .enex file and matches up internal links based on the note titles - but that won’t work for cases where you’ve edited the link text or the note. If you had only done that for a minority of cases, maybe the script could list the cases it couldn’t match, and leave them up to you to manually fix before running it again.
(the script might also incorrectly link some cases where the link text has been changed so that it matches the title of the wrong note. I don’t see any way to avoid that.)
Said script, or a second one, would then need to export in Joplin format somehow.