I done the same last year.
You need both 50 tawi (tax certificate), 1 for each company.
On your PND 91 enter the details of main company for 2022.
But upload both 50 tawi and use the totals from both 50 tawis for income, tax and sso deduction.
I didnt get advice beforehand, this is what I done and it was accepted and tax refund processed without issue.