It's really not clear what you mean. Layer modes can easily be switched in the layers palette, but it sounds like you want to actually retain the appearance of a blending mode, which may require extra steps like duplicating the layers involved in the setup before merging/ flattening them. anyway, you need to offer a better explanation of what you are actualyl trying to do.
If it's just to remove the blend mode in the layers palette and keep the current blend, maybe this method will help.
var LName= activeDocument.activeLayer.name;
executeAction(app.stringIDToTypeID("copyToLayer"), undefined, DialogModes.NO);
executeAction(app.stringIDToTypeID("mergeLayersNew"), undefined, DialogModes.NO);
var d = new ActionDescriptor();
var r = new ActionReference();
r.putEnumerated(app.charIDToTypeID("Lyr "), app.charIDToTypeID("Ordn"), app.charIDToTypeID(method));
var list1 = new ActionList();
executeAction(app.charIDToTypeID("slct"), d, DialogModes.NO);