A.B.
Absolutely see another doctor. In fact, you may want to take him straight to an ER.
My son woke up one morning (oddly, also when he was 2.5 years) screaming with pain. We took him to the doctor and they sent us straight to the ER. It turns out he had what's called testicular torsion. It's when the testicle can spontaneously twist itself (inside). It sounds like this could possibly have happened to your son. It's supposed to be incredibly painful and if it does get twisted and stays like that for too long, it could potentially affect his later fertility (on that side only).
The tendency for this to occur is actually genetic, and while it can actually be a relatively common diagnosis, it's almost never seen in kids this young (or so we were told by our doctors). It's usually something that would turn up in kids a little older (say age 7 and up). So that may be why his doctor missed it.
By the time we had arrived at the ER with our son, he was checked out by the experts and it was confirmed that's what had happened. It had also spontaneously corrected itself, which is why he was no longer in pain. Again, this might be what happens to your son (and why in the morning, he was better).
They still deemed it an "emergency" surgery, so we had to schedule it for the following week. If they didn't correct it through surgery, it could just keep occurring and potentially affect his fertility.
I had no idea something like that could even happen, much less what to look for, so we were very lucky they caught it. (The pediatric expert said he was one of the youngest cases he had seen.)
Once he had the surgery to correct the problem on both sides, they also found hernias on both sides. Poor little guy had probably been in some kind of pain for a while. :(
If this is what's happening with your son, it's an outpatient surgery. The toughest part was keeping a 2.5-year-old sitting still and resting for several days afterward. :)
I hope you and your little guy get this figured out soon.
All the best!