Many applications are involved in an apt-get run. The application showing you 
this question is for example debconf which is responsible for asking questions 
for the package dpkg works on which is called by apt-get. The --force-yes only 
influences the questions APT will ask you - questions dpkg will present you 
about config files are not included (question in which you have three or more 
options aren't really yes/no questions anyway…) and packages can ask very 
complicated non-yes/no questions, too.
Where are options to silence them to, see the relevant manpages for them (dpkg 
and debconf at least).

But, and thats the turning point here: That you see that question is
your own fault - as the question is included in your package, so i would
suggest you don't ask this question if you don't want them ;P


Beside that: Its really not a good idea to remove the running kernel - as the 
question already says - and i really don't see why you want that at all. Just 
imagine your new custom kernel build is broken and unable to boot…

-- 
Still get warning dialog with --force-yes
https://bugs.launchpad.net/bugs/669759
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