by Antistone
You've got spoilers for end-of-March in there. And presumably an oblique reference to something I haven't encountered yet, because I don't think the situation you describe can possibly arise using only stuff that I've encountered. (I've finished April.)But as to your question, my guess would be that an instruction to shuffle a whole deck implicitly captures all the cards belonging to that deck from anywhere on the board.
(In case of confusion, the end-of-March spoiler was...)
[o]That you get a variable number of epidemic cards.[/o]