Sounds like you deleted the data in the fields instead of deleting the actual related record. What method did you use to delete it?
There's a specific script step: Delete Portal Row that you can use to delete the portal row, if you enable deleting portal rows in the portal setup... dialog.
You can place a button in the portal row and specify that script step. You can also write a script that deletes the portal row after hilighting the portal row and asking for user confirmation. You can find an example of such a script inside the Known Bugs List database file. This script was specifically designed so that it can work with any portal and can be imported into any Filemaker file without needing to edit the script. All layout and table specific information is passed as a script parameter to the script. (You can also find examples in this file of how to use conditional formatting and tooltips with the delete buttons in the portals to make them a bit more user friendly.)
Thank you for your help.
I'll try enabling the Delete Portal Row in the portal setup and see if that works.