Some bikes shops don't see much electronic shift components. Perhaps your mechanic is one of them. Here, they have a lot of Di2 bikes. And when ever I talked to the mechanic that sold me my bike, we always got into a lengthy conversation and it sounded like Shimano provided endless help to him and other mechanics there whenever they had a Di2 question. So if your mechanic isn't getting in touch with Shimano on whatever regional level is appropriate. Then perhaps it should be encouraged.

However I too sort of think it's not related directly to the Di2. Just maybe a poor adjustment. Which in their manuals for Di2, Shimano give pretty good and concise instructions for set up. Did your mechanic follow those? Saying that he set it back to the default settings doesn't sound like he has a lot of experience with it.

Also might just be the bike got knocked on the RD and the hanger twisted a little.