I do believe the index mark is on the gear, not the crank itself.
the gear can only go on in one position, as it's keyed to the crank, is it not?
You can see the index mark in the counterbalance gear in this pic ... though the one for the crank gear is hidden under the oil galley tube.....
Edit:
If you are saying the shop somehow managed to make it so you can't see the INDEX DOT on the crank anymore, then that's a problem. if you look closely in this pic, you can see that the crank rod wrist pin end is just barely visible above the case - if you position yours relatively close to the same as ini this pic, the index dot on the crank should be on the "tooth" of the spring drive gear and roughly at 3:30 on the clock.
If you match yours to what's in my pic, you should be ok - as there are only 6 places you can put it - meaning the next position either way will be 60 degrees off.
What I don't know is if they can actually remove that 6 tooth spring drive hub from the crank? If so, did that put it back on in the right place?
I do know, since punching mine out and stroking the crank to be a 446cc machine, she's not as smoothe as she was due to the exta mass of the piston.
Hope this helps some.