Illustrator disregard spot colors inside of a pattern when placing document

I was preparing a file, where i've created a pattern with spot colors. While i was using this file on it's own, everything was fine, but my workflow required that i was placing this document inside of another document (template) that was created to send for the production company. 

After embedding the linked file, the spot colors used in the pattern object turned into composite / CMYK colors. I'm lucky the printing company realized this pre-press, otherwise it would have been an expensive discovery.