I'm writing in to confirm that this problem persists in Kubuntu 16.04.1.
I used a bootable Kubuntu usb key to install Kubuntu to an external
drive, and the installer trashed my grub configuration on an *unrelated*
internal Fedora hard drive.

Workaround in case anybody sees this:  unplug any hard drives that you
don't want the Kubuntu installer to touch prior to doing your
install....

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https://bugs.launchpad.net/bugs/1507448

Title:
  Kubuntu installation into external disk ruins internal disk boot
  whilst leaving external disk unbootable

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