File > Save: For single-scenario files (*.slim or *.sli extension), this will save the file to the latest version in all cases. For multi-scenario files (*.slmd extension), this will save the selected scenario to the latest version in the case that there are modifications to the scenario.
File > Save As: For all files types, this will save the whole model and all scenarios will be saved to the latest version.
File > Force Save All: This is useful for multi-scenario files. It will save all the scenarios in the model to the latest version, whether there are modifications to the file or not. Note that this means the results will be cleared.