Did the cafeteria plan reduce the taxes of the earnings tax on the original check where it was withheld?  Then the Deduction code was assigned a tax rule.

Now you are trying to reimburse the employee "ONLY" the cafeteria plan deduction?  Then you need to enter Manual Taxes as positives if you are paying him back for the deduction that reduced his original taxes.  This would be calculating manually how much that deduction reduced the taxes on earnings on the original check and how much the original check taxes would have been without the deduction.  Enter the difference in as positive manual taxes to correct the transaction. 

Which taxes to review depends on the tax rule used on the original check.  If it reduced no taxes for the cafeteria plan, no tax calculations are needed.  If they are reimbursed with earnings, the system will calculate the reimbursement with the earnings taxes.

The cafeteria plan reduces the gross then the system calculates taxes. When I reimburse as you suggested, the amount of the cafeteria plan does not record as earning and manual taxes need to be made at Data Entry time.  How can I make sure that this amount being reimbursed is properly recorded in the employees Employee's maintenance--- Employee Tax Summary-- and on the Quarterly Tax report.  Editing the Employee Tax Summary does not trickle down to any Quarterly reports.  the Tax Rule applied to this cafeteria plan id 805158 SECTION 125 EE DEDUCTION.

If you had earnings on the check, tax rule 805158 would reduce the earnings by the deduction amount prior to calculating the federal taxes.  I cannot say for the state without knowing what state.  Since you only are using a deduction code, there are no earnings to reduce so you must do the taxes manually.   If you want the earnings to show that you withheld the deduction which reduced earnings, now you are giving it back which would increase those earnings, you will need to edit the tax summary for the earnings it previously reduced.  On the original check I would increase the federal & state wages that it previously reduced.  If original check shows gross $1000, federal withholding $900 (which is what $100 deduction would show for original entry), change the $900 to $1000 if that is the only deduction that reduced earnings.  Then the Quarterly tax report should show gross - deduction = wages subject to tax $1000 and the deduction washed out.   This may require a support call if this is still confusing.  

If you had earnings on the check, tax rule 805158 would reduce the earnings by the deduction amount prior to calculating the federal taxes.  I cannot say for the state without knowing what state.  Since you only are using a deduction code, there are no earnings to reduce so you must do the taxes manually.   If you want the earnings to show that you withheld the deduction which reduced earnings, now you are giving it back which would increase those earnings, you will need to edit the tax summary for the earnings it previously reduced.  On the original check I would increase the federal & state wages that it previously reduced.  If original check shows gross $1000, federal withholding $900 (which is what $100 deduction would show for original entry), change the $900 to $1000 if that is the only deduction that reduced earnings.  Then the Quarterly tax report should show gross - deduction = wages subject to tax $1000 and the deduction washed out.   This may require a support call if this is still confusing.