Would you be okay if a quest that could have any time based component at all have an icon showing that there isn't unlimited time for this quest? Or are you asking for a pop-up every time some game state is about to change?
Time limits have to be communicated in some way...and have to be consistent. If at the start of the quest you are told you have five days or something then enforce that, if the quest says you must do this now, no time to waste, fine with that. But what you cannot have are arbitrary invisible lines during quests that flip an invisible switch from infinite time, to no time without communicating that to the player in any way.
