As a software engineer (among many other roles) I would suggest a software tweak is possible that would read the first pulse and bypass any code that expects two more. However, my experience is that unless this problem is very common, the effort (cost) would be prohibitive. Any question of responsibility aside, the practical solution may be to machine the notches back into the new (replacement) camshaft, thereby avoiding any further incompatibilities.
If the workshop are seeking the best possible solution for all, aside from re-sourcing a replacement, you may be able to forcefully suggest that a very faithful reproduction of the notches is required.