RTC backup by super capacitor estimation issue
You should calculate the discharge time based on the voltage across the capacitor decaying to the minimum value that the RTC can survive on. That voltage might be (for a guess) 1 volt. If your charged voltage is 3 volts then you can say this: -
$$dv = \text{2 volts}$$
You also know the current (50 uA) and using this well-know capacitor formula: -
$$I = C\cdot \dfrac{dv}{dt}$$
You can rearrange for dt: -
$$dt = C\cdot\dfrac{dv}{I} = \text{13,200 seconds or 3 hours and 40 minutes}$$
This is based on a 0.33 F supercapacitor.

If someone got an idea for why my RTC sink 50µA instead of 300nA

It's most probably the DFLS130L-7 schottky diode. Take a look at this graph in the data sheet: -

With power removed, the anode will be at 0 volts and the capacitor diode will be reverse biased at around 1 to 3 volts. At 2.5 volts reverse, you would expect to see 50 uA discharge current flowing in the diode.
Choose a different diode is my advice.