How to "dematerialize" a deck in the Magic Assistant card manager?
It looks like you can accomplish this by doing the following:


Open up the deck you want to convert.
Select the entire list of cards.
Right click and click Edit Card...
Change the Ownership dropdown to "Virtual" and click OK.
Copy the list of cards, and paste into the main collection.


This will result in each card appearing as physically owned in the collection and virtually owned in the deck. If you do this, you may want to also modify the deck's properties to make it Virtual so that cards you add to it in the future will be virtual.