No longer. preinitv6 now supports putting your startup scripts in /programs0/preinit.d. Then all you'd have to do is reapply hijack, reupload preinit (via FTP is fine), and recreate the /programs0 and /programs1 mount points (FTP is also fine for this) upon upgrade. It's not as nice as what you're looking for, but your scripts and programs won't get deleted.