After a distupgrade from debian squeeze to wheezy, kile kept messing around with the file encodings. Ignoring any values set in the “Open/Save” config dialog, kile took my UTF-8 files and saved them in ISO-8859-1. This is not as funny as it may sound, especially not if you use version control and LaTeX. Although I spend some time on this issue, I still don’t know the reason for this behavior. Nevertheless, here is a workaround that will delete your current config:
rm .kde/share/config/kilerc
Apparently, kile seems to keep an additional remark for each of the last opened files concerning the character encoding.
Obviously, this is my fault. I shouldn’t have done the update in the first place…