When you try to merge it, SmartAssembly will warn (when you hover over) that the assembly being merged has already been processed by SA and may lead to unexpected results. It will still let you go ahead with building though.
I think that so long as you don't apply any other options onto the assembly after merging it, and if the application isn't too complicated, there is a good chance that it would work out fine. Of course, what works and doesn't work is subjective to each application--the best way of knowing what will happen is to test it and see : )
Sorry to not have a more definitive answer!
Red Gate Software Ltd.