I have some additional tools in folder "scripts" incl. subfolders. On USB-update also the subfolders will be copied as empty folders (my USB-version don't use all tools from installed DO in scripts), so the script-folder should be ignored on an update (not on export of course).
It should treated the same as any other config folder.
If you choose to update both Opus and the config on the USB stick, the scripts folder should be copied to the USB stick.
If you choose to update only Opus, the scripts folder should be left as it was.
Is something other than that happening?
When updating to USB, the script-folder will not be updated, but non-existing subfolders will be copied as empty folders.
E.g. I have a "TrueCrypt"-folder in "scripts" in the installed version. After updating (not replacing) the USB-version there's an empty "TrueCrypt"-folder (there was none before). BTW I updated to v11.3 a few minutes ago, same behaviour.