Alternator troubleshooting

rframe

pǝʇɹǝʌuı
I've got a 2 year old Zeftronics regulator and a recently rebuilt Ford Mustang style alternator in my plane. It's worked flawlessly for 200+ hours and just recently I've seen twice where the ammeter was showing a discharge for a couple minutes and then it "came back to life" without requiring a reset of the regulator. Any ideas where to begin with troubleshooting?
 
It shouldn't be a factor if the alternator has been rebuilt recently but I once had intermittent output when the brushes were worn down so short they didn't always make contact.
 
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