There are two ways to get the filter to refresh:
A script with Refresh Window [flush cached join results]
Include the filter fields as part of the relationship--use the X operator so that they do not affect what records are related and now changes to the fields update the filter without needing a script to refresh the portal. Or, since you are modifying the relaitonship anyway, get rid of the portal filter and just include the filter fields as regular match fields in the relationship. Both approaches have advantages and disadvantages so take a careful look at how the approach that you choose affects the use of this same relationship in other parts of your database.