Quick confirmation that this is a deliberate change:
Keep your spare tokens handy for those hard to remember hidden information.
UPDATE: The Rules Reference has the up-to-date definition of derived information:
Derived information is any information about the game, game state, or cards one or more players has learned through the process of deduction. This includes card that has been chosen for Femme Fatale, a card hosted on another card, etc.
Derived information may be marked with the use of a token or other indicator so that players remember the information. A player cannot misrepresent derived information or hide the open information necessary to discover derived information. Until a revealed card enters a hidden or randomized zone such as HQ or R&D, then it is still uniquely identifiable and considered to be derived information.
So tracking cards in R&D (Indexing), etc. is not permitted.