Did you do the original return in ProConnect?

Did you input the return, as originally filed into ProConnect BEFORE trying to do the amended return? 

Both of these questions affect how to an amended return. This article may help

I entered the original return in tax year 2018. I'm doing the amendment now in 2020. When I enter the original amounts from the Schedule A (from the 1040), the number is calculated the prorated amount for part-year residence, which also impact the net income calculation. All other amounts are fine.

Did the original include a part year MD return? 

Have you checked the 502 instructions for part year returns? The software may be doing it correctly. For MD part year returns you do not get to specifically allocate deductions.