I was editing files with geany that are located on an FTP server. I have done this with geany before and never had a problem. Recently, I went to save a css file for a page I was working on and geany crashed. Upon reopening the file, it was totally empty. I have a few plugins installed but, I wasn't using them. I recently started using Thunar to connect to ftp.
Plugins installed:
geanylipsum.so
geanypg.so
geanymacro.so
shiftcolumn.so
webhelper.so
OS: Debian Wheezy 64-bit
GTK 2.24.10, GLib 2.32.4
Geany 1.22, en_US.UTF-8
Please read the wiki article http://wiki.geany.org/config/all_you_never_wanted_to_know_about_file_saving and post which settings you are using for saving the file.