Is everything you want/need in the "external" user account?
If so, do you "lose nothing" by deleting the [old] internal [drive] user account?
If the answer to both of these questions is YES, here's how I'd do it:
(probably an entirely "roundabout" way, but it should work)
First step:
Log out of your external account (for the moment).
Log INTO your [old] internal account.
Next:
Run migration assistant to see if it is able to find the "external" account.
If it does, DON'T attempt to transfer it yet. At this point, we are "just checking".
Quit migration assistant and go to next step.
Now:
Open up the "users & groups" preference/settings pane.
Click the lock and enter your administrative password (for the old account).
Now, click the "+" sign at the bottom to create a NEW account.
This is going to be a "temporary" account, so give it a name/password that is fitting. It IS NOT going to be the "main" account.
WHY we are doing all this:
Every account has an "ID number" that is assigned by the system.
One SHOULD NOT be fooling with it.
However, there are ways to control which account gets assigned "the first" ID number, which is 501.
Your old internal account probably has that number.
The new temp account should have ID 502.
(you can check the ID in "advanced settings")
OK, next step:
LOG OUT of your old internal account.
LOG INTO your newly-created temporary account.
I believe you again have to click the lock icon and enter your password.
Now:
Click on the old internal account to select it.
Then, click the "-" sign to DELETE the old account.
You want to delete it completely -- NOT "archive" it or anything like that.
Now, "the space" that the old account occupied (ID 501) is "empty".
Now that the old account is gone...
Open migration assistant.
"Aim" MA at the external drive that has the "external" account.
Give MA time to "digest" everything.
Assuming you can now see your external account in MA, select it and choose to "bring it over" to the internal drive.
Give MA time to do its job.
When done, the external account should now be internal, AND, it should have the ID 501 as its account number.
Now, LOG OUT of the temporary account and LOG INTO the migrated account.
Look around and make sure everything is as it should be.
That's how I'd do it (but I guess that's just me).
Good luck.