Hi Jason,
in such a case I would assume that it will be required to call copy-sidebysidefiles to ensure that the updated javascript files are copied into the version directory.
Alternatively you could just enable the side-by-side functionality while updating the farm. After the farm has been fully updated you could disable the side-by-side functionality which will ensure that all servers again use the latest version of the javascript files in the layouts directory.
Cheers,
Stefan