Haas Bioroid's version of Chronos Protocol: Selective Mind-Mapping reads:
"Whenever the Runner trashes a card for brain damage, he or she removes all copies of that card from the game (installed, in the heap, stack, or grip). The Runner shuffles his or her stack."
|Yes, the list is not comprehensive, you have to remove the copies from wherever they are in the game.|
This is the first confirmation that reminder text might be in use in Android: Netrunner, although it is not clear which cards use parenthetical reminder text or not.