I haven't really thought of the pros and cons in detail. But having an initial version and then copying it, running it in update and modifying it is what I do. This suits me best as it also helps me compare the differences and I find it aesthetically better too.
cdn my rule of thumb is add patches to the current script and for new versions i.e 8.1 goes to 8.2 copy the existing script and name myscript8_1, archive off myscript8_1 and add the 8.2 changes to myscript.
This will be impacted by size and complexity new versions (we are completely redesigning our system in Feb2005 so we will create brand new scripts).