The Employment Allowance is an "Employer Level" Chart of Setup Setting and it doesn't come under the purview of "Employee Migration".

The Eligibility rules for the Employment Allowance have changed drastically from April 2020.

As from 2020/2021 claiming of the Employment Allowance is subject to the claimant making a correct de minimis State Aid declaration. Without making a de minimis State Aid declaration through Employer payment summary (EPS) submissions, you would not be entitled to the Employment Allowance.

Also, Employment Allowance claims will need to be submitted each tax year. Claims will not automatically roll over from the previous tax year. If the Allowance is not activated even after you've made the declaration through EPS presumably from your previous software, then you need to raise the issue with HMRC.