Thank you for your help! I think I figured this out. It boils down to this: an LLC with only one member is treated as a sole proprietor for tax purposes, so in essence, the income (1099) has been reported to the EIN of one of them who then makes a 1099 for the other person and they each have been doing their tax preparation as sole proprietors, each preparing a schedule C. 

For some reason they registered with the secretary of state as an Limited Partnership, but they really are not a Limited Partnership since the limited member has been working just as the general member....

Thank you for all your help.