It should be added at the end of the file, actually if you want the honest truth, you should not be making changes to the acad2000doc.lsp, but rather put it in acaddoc.lsp (if there is not one, you can create it and put it in the support path)
It is likely the command line suppression in the acad2000doc.lsp will limit the things you can see on the command line during load anyway.
If you want to purge the drawing, you should add another line to the lfd lisp to do just that. A simple purge macro should do the trick:
(vl-cmdf "purge" "a" "*" "n")
Make sure you put the save command after the purge or your changes will not be saved in the initial save after opening. In fact you may want to change the save line to "qsave" because I think there are a couple of instances where save would prompt the user resulting in AutoCAD pausing for user input.