There are a couple of options. 

Option 1.  In 2020 you could change the deduction amount to be withheld.  For example, if the amount from the carrier is $50/month the formula for 52 pays would be $50*12 months / 52 weeks.  For 53 pay periods it would be $50*12/53 weeks.  The amount can be changed in the benefit setup or in the setup of the employee configuration > conversion factor.  Change the amounts back once the 53rd week is paid.

Option 2. When the deductions were created, verify if they were set to a unique frequency, for example 13 pays per year (the frequency doesn't mean it will be paid 13 times per year, but rather considered it a grouping.  It could have been called A, B, C or 1,2,3 instead of weekly, biweekly, monthly, etc.).  When calculate payroll is run throughout the year, you would select the earning/deduction frequency for the unique frequency (ie. 13 pays per year).  When you are processing the 53rd pay period (when you do not want the deduction to withhold, do not select this earning/deduction frequency).    This option would require a review of your earning/deduction setup to see what earning/deductions would be included in the frequency that your select. 

Option 2 is the recommended option.  If your earnings/deductions frequency was set up to float or another frequency that is not unique or does not work with the frequency of other earnings/deductions, you can reach out to your channel partner to see if they will change the frequency in SQL for the affected earnings/deductions.

Option 3.  Run Update earning and deductions to calculate no for the deductions after the 52 pay, but prior to 53 pay.  After 53 payroll is posted, run update earnings/deductions to calculate yes.  You will need to manually set anyone that should not calculate back to No.  This option requires reporting on who should have the deductions calculate Yes/No.  It is strongly recommended to do a backup prior to running the update earnings/deductions as this has the potential of changing a lot of information.