Switch from paper filing to eFile caused my overpayment carryover from 2019 to be not carried over in IRS system, how can I correct this error in IRS system?

to simplify the response when did you file 2019? was it e-filed or mailed? if e-filed did you get an acceptance e-mail? also, review the transcript of your 2019 return. if it doesn't exist that would indicate that either the IRS never got it or it has not yet been processed (unlikely unless you filed it very late)

Do you mean you wanted some or all of the 2019 refund applied to the 2020 return ?    If so did the amount to be applied show up on the 1040 page 2 ?   Did you ever get the refund ?   Was the return ever processed ?