How to save pdf which contains pantone colors properly?

Hello everyone. Here is the problem:

I'm usually doing my artwork in CMYK colors, but one of my customer's concepts require two Pantone colors. I use Pantone colors from swatches library and save print ready file as pdf. But, after sending a file to typography I get my file back with the message, that there are no Pantone colors - I used CMYK colors. I don't convert any colors to CMYK before saving, I googled about it and I'm pretty sure I did everything right. I called to guy from typography and he told me how to convert colors to Pantone. I did as he told me, but the result is still the same - Pantone colors are gone in final pdf. Is that possible, that after saving in pdf there is somewhere checkbox, which converts all colors to CMYK? Because I do another work for this client I don't want to face this problem again - so If anyone has any idea, what is the problem, I will be very thankful for your answers.f that question

Thanks