During the upgrade you were asked to either keep the version of
05_debian_theme you had modified or to install the new version, because
you choose to keep the old version you did not receive the change that
would have removed the GRUB_PREFIX line as Colin mentioned.  In the
future one thing to do would be choose "show the differences between the
versions" to inspect the changes between the files and make a decision
after that.

Here is the relevant bit of the upgrade log:

Configuration file `/etc/grub.d/05_debian_theme'^M
 ==> Modified (by you or by a script) since installation.^M
 ==> Package distributor has shipped an updated version.^M
   What would you like to do about it ?  Your options are:^M
    Y or I  : install the package maintainer's version^M
    N or O  : keep your currently-installed version^M
      D     : show the differences between the versions^M
      Z     : start a shell to examine the situation^M
 The default action is to keep your current version.^M
*** 05_debian_theme (Y/I/N/O/D/Z) [default=N] ? n^M


** Changed in: ubuntu-release-upgrader (Ubuntu)
       Status: Confirmed => Invalid

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https://bugs.launchpad.net/bugs/1078653

Title:
  GRUB_PREFIX not set after dist-upgrade

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