Multiple 1099s for same contractor because of payroll provider change

@Critter-3 knows quite a bit about payroll. Stay tuned.

There is nothing wrong with doing so and it is the correct way to handle it even if the EIN did not change.  

You, the business owner, are only required to file one 1099-NEC for your subcontractors that shows all their payments for the year.  However, if the records are in multiple places, and it is easier to send multiple 1099s, that's not a problem.  You might want to let the contractors know what to expect.  (The total should equal the overall total for the year, of course.)

May I ask.....you are using a payroll service to pay 1099 independent contractors?   Do you also pay employees that get a W2?