Hi Wilbert,
Thanks for your reply.I have seen first hand it removing tables under SYSTEM user as well as changing privileges and such. WE have restored once an SPS7 rev 70 on SPS9 rev 92 and some of the default system privileges were revoked and had to be re-granted for instance for the hana cockpit.
Then again when we restored Hana 92 on 112 with XS Advanced enabled, all XS Advanced default schemas were gone as well as a few others that were added in SPS11. It actually killed XS Advanced when restored on it. The service was red 
Yes my colleagues were saying the same thing about i never had an issue as well but I don't believe it anymore having seen these issues pop like this even on default base installation before I add any of my own things 