Just to make sure we're on the same page, the 1.0 CE item (Onion Helm) came on its own code sheet (same as Garlond Goggles did for Standard edition). I know this as I personally bought/redeemed both. Both editions come with a code for the game, but it was activating the extra item code that made it CE/Standard (as well as all the other physical stuff in the box).

With 2.0 they changed this and Collector's Edition actually has a different main game code/included the items, unless you upgraded on the Mogstation later. When they gave free upgrades to 2.0 CE they were basing this on if you had the Onion Helm code on your account as that's the only way they can tell which version you had.

From what you've written in the subject, it suggests you tried to add the (somehow unused?) main game code and it created a new service account (which it would as each game code is a separate copy of the game/subscription). As mentioned above with 1.0 the game code doesn't determine whether it's standard/regular, the extra item code sheet does. You need to add the code for the Onion Helm specifically which is what SE was trying to explain to you.

If you have added the Onion Helm code, then what happened? Did you have the Onion Helm before? Do you have it now? Did the extra 2.0 CE items not arrive?

But realistically you should have been asking these questions 4 years ago when 2.0 came out. Heck even 2 years ago when 3.0 came out...