You are removing Kits, not the chroots. You need to remove them in the
Ubuntu section

** Changed in: qtcreator-plugin-ubuntu (Ubuntu)
       Status: New => Invalid

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https://bugs.launchpad.net/bugs/1512272

Title:
  Cannot delete a chroot from ubuntu SDK

Status in qtcreator-plugin-ubuntu package in Ubuntu:
  Invalid

Bug description:
  I follow "Tools/options", then "Build & Run", in the "Kit" tab,  I try
  to delete the install chroots there by select "remove", but in the end
  the chroots are not removed. Re-launching the SDK still see the
  install chroots there.

  This happens on 15.04 desktop.

  liuxg@liuxg:~$ dpkg-query -W ubuntu-sdk qtcreator qtcreator-plugin-ubuntu 
qtcreator-plugin-ubuntu-common
  qtcreator     3.1.1-0ubuntu9
  qtcreator-plugin-ubuntu       3.1.1+15.10.20151018-0ubuntu1~0vivid1
  qtcreator-plugin-ubuntu-common        3.1.1+15.10.20151018-0ubuntu1~0vivid1
  ubuntu-sdk    1.221

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