Change the tax profile back to what it was when it was incorrect.

Reverse all checks that were incorrect and update.  In Sage 100 current versions you have a reverse icon beside the entry # field under employee name in Payroll Data Entry. 

Change the tax profile to the correct state and manually enter new checks with manual tax selected and 'A' or something else at the end of original check # on correct checks.

The reason to enter them manually and use manual taxes is so you can control the total tax amounts distributing into new tax fields correctly.  Any discrepancy can be added or subtracted from something like federal or state withholding without causing issues in other tax fields.  Make sure the employer taxes are correct before updating the corrected checks.

Please verify this suggestion so others can benefit from the answer.