I may be getting fuzzy at the end of the day and after lots of clicks and staring at this, but it seems like all the fields on 8949 can be overridden, so it is allowing me to enter a negative gain (for the QOF deferral), and then I could complete an 8997 manually and file the return on paper. Not a great solution, but at least I wouldn't have to convert to a new app this year.
