I am having this same issue and even after following the instructions here, I still get the same warning message.  I am trying to re-organize mainly all income/cogs and expense accounts.  Is it possible that if I have used some of these accounts for 1099's in the past and that is why it is preventing me?  The only thing I have not tried is removing the check box from all 1099 vendors where it asks if they are 1099 eligible.  I have several in that list so I'm hoping I could avoid doing that.  I have also tried to turn 1099s completely off in preferences - even after "omitting" all accounts from 1099s.  And I have also gone through all 1099 eligible vendors and removed any pre-filled accounts from their account settings.  I'm on QB Enterprise v20.