Non B Visa And Holiday

I'm a bit confused.

I'm going back to Holland for 2 months. I was checking out what I needed to do to keep my workpermit valid since the 3 months run out while I'm in Holland. "Very easy" said my accountant, I just make an early visarun before I leave and she would then extend my workpermit. A bit later she calls me back saying that my Non immigrant B visa with multiple entries will be taken from me when I leave Thailand. I thought this was a bit strange since I have been leaving the country every 3 months for the visa run these last two years and it has never been taken from me. She said she could go to the immigration office on Samui for me to get a special stamp, costing 5000B. This way they wont take my non B. To me this all sounds a bit strange?!?!

Does anybody have experience with this or know anything about it?

Thanks for your help.