How to bypass validation rule in Case object on Merge Case scenario only ?

I have a validation rule that prevent SF user from updating Case record if that case is handled in Other application. Validation rule limit user from updating by checking if updating user is in AllowedUser list or not which is in Custom setting.

 Rule is working fine but in case client send a duplicate Case then we need to use Merge case feature. Now the problem is that Validation is blocking it from merging since all it does is update and delete. How ca we by pass validation rule in Merge case scenario.