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The last update of the Rules of Golf (2008) removed the rule that said playing a wrong ball in a hazard didn't count! It is a 2 stroke penalty in strokeplay, loss of hole in matchplay whether from a hazard or not.
The penalty for playing a wrong ball in strokeplay is 2 strokes, regardless of how many strokes you have with a wrong ball.
You haven't said if the original was found or not - I assume it wasn't, so if he then played the provisional as his fourth stroke, whatever he scored with that ball, he...