Would it be possible to get a symbol like the signed, foil, etc drop down ones to show that you have a card in your collection but you do not currently have it available? Like if it's getting signed, you loaned it to a friend, something like that. I frequently use Deckbox on the go to see if I have a particular card and being able to see at a glance that yes, I do own it, it's just not in my collection at the moment, would be very useful to me.

In the meantime you could create a deck for each use and add/remove cards to it as appropriate.