Why am I getting an Incompatible global variables after creating a protected reference model?

1) A reason why you might get that error is if the parameters are in the function's workspace so they are not accessible to the model. You can resolve this issue by including the following in your function:

>> assignin('base','name_of_var', name_of_variable);

>> var1.Value = [1 2 3 4]

It is a 1x4. If you then try to use the protected model using a "var1" with different dimensions like

>> var1.Value = [1 2]

you will get an error saying that the variables used by the protected model are incompatible with the variable that existed when the model was created. This happens because the files generated when creating the protected model have the dimensions of the Simulink parameters hard coded.