Hi Daveromine,
May I know how you are generating rows for the repeating table that will show the differences between the two lists? If you do not have this logic yet, you may want to try out qRules. This is a very powerful tool you can use for inserting rows, setting specific values for rows (dynamically), delete rows, etc.
Another appraoch you could use is a double eval technique for concatenating multiple rows into one field. What you would need to add here is a logic that will determine similar rows and exclude or include them in the target field.
Regards,