Capacitor as power buffer for battery change
R1 in your circuit limits the charge current when you connect the new battery. It is not related to the discharge time (as the &quot;equivalent resistance&quot; of your RTC is much higher).
Your capacitor holds 3.3 mC (3.3V x 1mF) and will hold 1.3 mC when discharged to 1.3 V.
Assuming a 5uA discharge, this means 6 minutes and 40 seconds. Since you mentioned this is the max. current, it seems fine from the info you provided. You could test the discharge rate of the open capacitor to check the leakage current.