@JFKX The only way that progress would be lost in changes like this is if you deleted the Xbox account from the EA account. Simply changing the email that is used to log in would not cause data to be lost.
If you change the email on an account, you can use that email to create a new EA account yes, but you would have to manually delete the Xbox account from the original EA account and link it to the new one. That isn't something you can accidentally do since you have to manually unlink the console in your EA profile online.
What it sounds like is, if other games' progress is still there, and it's just GW2 that is not, it would be a sync issue, or it was not actually linked, or the Gamertag was removed. There is no way to manually delete that progress because it is server-side and not stored on your console. That kind of rules out being delinked though since every other game still has progress.
There are Xbox steps you can try and see if it works but sadly if they do not there is no restore data option due to the age of the game.
I would log into your EA account online on EA.com go under connections and make sure everything is linked to the right accounts.