I think there is a bug in Gurobi where, in certain cases, after modifying a model, resetting it, and optimizing it, the model returns the results from the original unmodified model instead of the new model. I have a reproduction of the error (a C# project), see attached.
Looking at the log file, it seems like the barrier algorithm isn't even invoked for the modified model.
As far as I can tell, it only happens for QP models when Presolve=0 and Method=2 or -1. If you run the test, it will pass for all values of Presolve and Method except for these values.