2003 Honda Accord Alternator Problem

I took my 2003 Honda Accord in to have the rear brakes replaced. They told me that I needed to replace the pads/rotars on the rear; the pads on the front, (3) of my four tires and the battery. I have since replaced the pads and rotars on the rear brakes, the pads on the front and the battery. I didn't replace the battery right away which caused me to fail inspection (car wouldn't hook up to machine) therefore mechanic said it wasn't ready. Then the car kept having trouble starting. Therefore I had the battery replace. Then I began hearing an excruciating noise from what I thought was the serpintine belt. I had a mechanic look at it and he said it was the alternator. It made the noise for two weeks straight then it stopped. My question is "Could the problem have corrected itself or am I in danger of something worst to come?"