Hello Jiří,
Can you check with the latest dpkg. I think this was fixed between 1.13.13
and 1.13.17 (probably by Ian Jackson in 1.13.14, have a look at #351361 or
#108587).
At least with a testcase similar to what you describe, I get:
Configuration file `/etc/test-package.conf'
==> Deleted (by you or by a script) since installation.
==> Package distributor has shipped an updated version.
What would you like to do about it ? Your options are:
Y or I : install the package maintainer's version
N or O : keep your currently-installed version
D : show the differences between the versions
Z : background this process to examine the situation
The default action is to keep your current version.
*** test-package.conf (Y/I/N/O/D/Z) [default=N] ?
Kind Regards,
--
Nekral