Did you ever get this resolved?  I am having the same issue.  One partner left and a new one came in, so it wants me to enter % of ownership just before the one partner left and just before the other joined, however then the K-1 form do not show the correct ending (for partner leaving) and beginning balance (for new partner).

Is it possible to just override the warning and efile anyway?

I did manually calculate the K-1 amounts for each partner, so those are correct and are not an issue with showing an error.