That switch keeps the Bonus Advance relay locked in until the Bonus Advance unit takes a step. When the Bonus Advance relay fires it closes a switch that sends power to the Bonus Advance unit Step Up solenoid. Usually that solenoid will fire instantly and open the switch shown above, cutting power to the relay and ultimately to the solenoid too. The current required is high but lasts only for a fraction of a second.
If the Bonus Advance unit solenoid somehow isn't moving or isn't opening the EOS switch the relay stays on indefinitely, keeping the solenoid on with it. In this case the current required is high and persistent which is more than the transformer was designed for. In this situation the high current demand is putting strain on the transformer which drops its output voltage everywhere. The GI is what's easily visible. If you put your meter on the 50 VAC output you'd probably see that drop too.
First I'd check that your fuses are the correct value, then figure out why the EOS switch isn't immediately releasing the Bonus Advance relay.