[strictlypersonl]

First, bypass your Master-Disconnect switch. If it is marginal, it might give you similar characteristics (if it cuts off the alternator power).

It could be intermittent/bad ammeter or its connections.

I would also look for an intermittent short somewhere. Probably close to the alternator main wire (could be internal, too) since it's apparently not showing up on the ammeter.

The next this happens, you really should immediately use a voltmeter to trace where the power is not showing up.