Theory behind parallel battery with diode
The battery model in most simulators (I don't use Multisim) is not really a battery, it's an ideal voltage source. So this circuit will simply very quickly discharge the capacitor to 48.7 V through the ideal source. 

If it were a real battery, the current flowing into its cathode could conceivably damage the battery, depending on the battery chemistry and various other factors.

It seems likely that you really should arrange your "protection diodes" to protect the battery from reverse current, rather than the capacitor.