If it was the same type of stem from the same company then I'd expect an even swap. I've never paid for a stem change. For example, on the Roubaix I bought last year, as long as I chose a similar quality stem and not a carbon stem or upgraded stem I was free to swap until I found one that fit me correctly. I spent a total of about 3 hours on a trainer at the shop getting it dialed in.

I did have to pay for a saddle swap because I'm a big guy and it required a significantly wider saddle than was available in the standard saddle designs.

If you upgraded stems and didn't just change the length I would expect them to charge unless you worked a deal in advance.