How to figure out if a 25V capacitor can replace 50V in this circuit
The best way to know for certain would be to measure as you did (although you said 'where it would have been' which might suggest you had it removed).  In this case since the highest voltage source is 5V, and there is no boost converter topology present to increase the voltage (you would need an inductor to do that), the cap would never see more than 5V.  A 25V rated cap would be perfectly fine.

In general, if you rely on measurement though, be sure that you check it under all possible operating conditions.  Ideally you should understand the circuit well enough to know what potential voltages (and current) may be present at any given component.

EDIT: If you plan to take measurements (of a non-steady-state circuit such as this) to confirm your expectations of peak voltage on a cap, it's probably best to use a scope if possible, since meters won't reliably capture brief pulses or transients.