I suspect that auto-partitioning with multiple disks has always been a
problem, but wasn't so serious previously, since the user would just be
warned about having more operating systems on the disk than they really
had. It became more dangerous when combined with Windows not being
detected. A two disk setup of first disk with (undetected) EFI Windows
and second disk with Ubuntu is handled as a "single OS Ubuntu upgrade",
and when the user clicks to upgrade, the Windows disk is wiped.

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https://bugs.launchpad.net/bugs/1265192

Title:
  Install/reinstall wipes out all/other partitions

Status in elementary OS:
  New
Status in “ubiquity” package in Ubuntu:
  Triaged
Status in “ubuntu-livecd-image” package in Ubuntu:
  Confirmed
Status in “ubiquity” source package in Trusty:
  Triaged
Status in “ubuntu-livecd-image” source package in Trusty:
  Confirmed

Bug description:
  Brand new Samsung laptop with UEFI. I had installed 13.04 Ubuntu but on 
reboot I never saw the 'grub' style menu. It just kept going into Windows 8.1.  
So I got the 13.10 version (64 bit) and choose "Reinstall Ubuntu" (That may not 
be the exact text)
  It removed all the partiions including the recovery partitions. I do have a 
backup for the windows install, but I was very surprised that this happened.
  On a positive note I now have Ububtu up and running on my machine. 
  This is not my first time with Ubuntu. I have installed Ubuntu alongside 
WinXp, Vista and Windows 7. I've used Ubuntu desktop for over 6 years.
  If you would like me to try something to replicate this. .. I could shrink my 
existing partion make another one - reinstall and see if it whacks that one. I 
can do this now .. I'm still moving into this laptop so starting over is not so 
bad.

  Steve Devine

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