I would argue to say nothing about having too many miles, but not spend them.
It is very likely that the airline will sooner or later figure out what happened and automatically remove them. If you had already alerted them to remove the miles, and then along comes a program to remove them, you could have them double-removed. Then you would have to call again to get them reinstated. Then they might just think something fishy is going on with all the to-and-fro ing of miles. Why put yourself in that position and make the airline's problem your problem? At the same time, you are under no obligation to spend any miles improperly credited to you.
Perhaps once the time limit (6 months, 1 year, maybe) for asking for back credit has expired, you could either alert the airline, or just donate them to charity. If you've reached a point where it is too late to ask for miles, it would seem fair that it is too late for the airline to take them back. At this point, it would be too late for an automated system to remove them, so you presumably wouldn't run the risk of having them removed twice.
Last summer, for instance, I flew an award ticket where I had to change the routing the day of departure. As a result, I was credited as though I had flown the routing, with a Y fare bonus no less. Sure enough, the miles and EQMs were deleted within a week without any action on my part.