After the fact payroll problem
How can I transfer paychecks I have issued to employees as "Vendors" to Payroll?
How can I transfer paychecks I have issued to employees as "Vendors" to Payroll?

You can't transfer them. You need to recreate the payroll checks using the same check number as the actual ck they received then void the checks paid to the employees (as vendors).
You don't have to use after the fact payroll, you could just edit the deductions in the payroll check detail screen but don't print the checks, just assign the check numbers that your employees actually received. Make sure to use the correct date the checks were written as well.