How'd you get that initial short year one efiled?

The first short year should have been filed with 2019 software for any fiscal year ending in 2020.  So you might try deleting that return so Proseries has no record of it.  I don't think IRS is rejecting it, but merely Proseries.  Then refile fiscal year ending in 2021.

So basically because even though the short year was all in 2020 I really should have filed using the 2019 software...

I filed it using the 2020 software, but I guess I should have used the 2019 software