Importing a portfolio into another portfolio creates a copy, so once you save the combined portfolio you can delete the individual ones if you wish.
Also, if you have a portfolio open and want to add a new character to it, there is a Create New Character option under the Portfolio menu as well - or you can import characters from the Encounter Builder or an Encounter Library into an existing portfolio.
Finally, if you want to customize a character and then have a number of identical ones in the portfolio, you can build the first one and then use the Duplicate option on the current character in the Portfolio menu.
I do this same thing running my game; I have the individual portfolios that I get from my players, and I combine them into one portfolio called The Party. Then I import each encounter into that portfolio to use the Tactical Console, and when I'm done with them I use the Delete All Enemies option to prepare for the next encounter.
Currently Running: Pathfinder Second Edition
Currently Playing: Pathfinder First Edition, Star Trek Adventures
Former HL Games: D&D 4e & 5e, Mutants & Masterminds 2E & 3E, Savage Worlds
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