I do my research in the ancestry online interface, since I find searching from FTM to be cumbersome and excruciatingly slow.
So, when I first opened FTM in the secondary profile, it saw my tree as not linked. I downloaded and now sync ONLY from the secondary profile. That way I did not lose any of my invitees - some of my cousins had a hard time understanding how to do it the first time. I did not want to put them through that a 2nd time.