I upgraded to OS X 10.7 this morning and upon attempting to connect to my corporate VPN, I discovered that my script at
/etc/ppp/ip-up has disappeared. Has anyone else encountered this problem, or do you know where it might have ended up?
It very likely got overwritten. The upgrade does nothing to back up what it considers "system files" and simply overwrites them with the latest version.
Another good reason to do a full backup before upgrading.