Transferring cleared payroll data into a different company file

There is no way to transfer payroll transactions from one company file to another - because there is no way to import payroll transactions into a company file.

The only way forward is to very, very carefully recreate the paychecks in the correct company file so they're exactly the same as the ones you issued.

Do you mean to recreate the checks in Payroll and just mark them as "to print" instead of direct deposit? I'll be asked to send the payroll data to intuit when doing that, what will the repercussions be regarding taxes that have already been paid on the previous direct deposits if I send these duplicate checks to Intuit?

If they're direct deposit checks then that is harder. In this case, make sure they are not marked to be direct deposited, and then add a net deduction to each check for the DD amount. That deduction should use the same account that your DD items use.

And then you'll also need to re-create the transactions that Intuit normally creates in your file when you send the DD checks - transfers from your bank account to the the DD holding account.