Hi,
You can try using save_system for saving your simulink model.
Also, you can refer the documentation of save_system to learn what all parameters it can take. For example:
% Save the model, save the model workspace, break links to user-defined library blocks,
% and overwrite if the file has changed on disk,
save_system('mymodel','mynewmodel','SaveModelWorkspace',
true,'BreakUserLinks',true,'OverwriteIfChangedOnDisk',true)