Here is an update on this ticket. After taking out the winter wheat and working on the model for a while, I identified that SWAT+ Check is not reading the output files correctly when it is filtered for agricultural land use and is showing 0.000 for plant uptake, wrong biomass numbers, and NA for N and P removed in yield. After looking at the nutrient balance and yield files, there is uptake, there is N and P in the yield, and the biomass looks correct.
As far as the winter wheat goes, the phubas0 value does still flatline, but there is still biomass present leading to yield. Not sure what to do about that, but as long as you are not harvesting for grain, it should be okay.
If anyone has suggestions on how to reset SWAT+ Check or fix it somehow, please let me know!