Hello Mohammed,
The problem you presented can be solved by using MATLAB Cosimulation. It means to run multiple sweeps/iterations in Optisystem through MATLAB. In this way, you will have the results of your individual iteration stored in MATLAB no matter if you cancel the simulation at any point. Please try to follow the following .m and .osd sample files to see how MATLAB Cosimulation works with OptiSystem:
MatlabOptiSysBER.m
OpticalLinkProject.osd
Good Luck.
Cheers,
Ahmad