It may or may not make difference since your engine balanced internaly by the balance shaft.My concern would be balancer coming apart if theres seperation between the rubber and and metal disk that makes the balancer.I have rebuilt alot of engines I never used a balancer that wobbled.I would do a google search and see what info you can find out.One thing that could happen is you can cause an oil leak

 

If the outer ring of the balancer is moving...it needs to be replaced. The outer ring will bounce around and could very likely mess-up other things.

Is the engine still under warranty? If so, makes me think the mechanic/friend does not want to do a warranty (free) repair.

 

Other things like causing the crankshaft to be out of balance which can also cause the engine to start knocking.You said its been like that for about year I believe,Im surprised that no dame has occured already.