I am trying to have one pex_executable for a file and a folder, however the folder is not packaged into the pex file. How do i explicitly tell pants to load the folder as well?

My understanding is that you want the folder to be embedded inside the PEX. Is that correct? In that case, you could try adding the folder contents as resources

Yep, depends what's in the folder. If it's resource files then this is the way to handle it. And you add an explicit dependency on the resources.