I think that you can remember what a track sounded like, even if it were a few weeks ago - especially if you have played it over and over and analysed sections / passages . There a few tracks that everyone, I am sure, knows exactly how they sound on their own system, compared to say, someone elses.
Ive recently changed a lot of my set up and i played an album that I hadnt listened to since I changed my kit ( the last time id heard it was with my old set up). It was Hotel California - i could spot all manner of differences immediately. So my memory had stored what it sounded like previously and compared the two. It seems that too many people reckon that you cannot percieve these, sometimes delicate changes, but I believe and trust my hearing and interpretation of such, to say that I can (or think I can hear them) and thats good enough for me. On the matter of leaving something on for a period of time, i would say yes, there has to be some warm up, but the only way to find out however, is to give it a go and then make a judgement call