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