That limitation of enex files doesn't just apply when importing enex into another note app, it applies to importing to Evernote itself. Yes, that means for Evernote users, their enex backups are not lossless - in the event an Evernote user needed to restore those backups to Evernote, that user would lose all their note links. With all their resources, they couldn't figure out how to create a lossless backup. I guess they were too busy trying to settle on the perfect shade of green and shape of elephant head logo.
I wouldn't bother trying to recreate any note links before getting this plugin: Quick Links Plugin
That's a game changer for speed of recreating note links.