This is probably an ultra-rare and low-priority issue to fix, but I'll still let you know.
If you export a script, then export another one replacing the first one, the two get merged instead of the first one being replaced if the latter has a different structure (e.g. the first one is just a single file and the second is a package). So you'll end up with an .opusscriptinstall file that contains both scripts (or parts of it) in one.