This is a actually a pretty common way to engage/disengage it when you're on the trail and either the motor quits or switch malfunctions. You can in fact manually do it without any problems.
It will stay engaged and will not be a problem, as long as you reinstall the motor. This way the locking fork will not be able to slide between locked and unlocked inside, and will stay in the locked position. I've done this more than a few times.