What cheesehawk says is correct. If however you don't want to manually edit the files, you can force Steam to re-download the original ones for you.
In such a case, follow the steps below.
When a file is missing you can run a file integrity check through steam and it will download it again and place it in your game folder.
The CoD settings are kept in three files: conf.ini, confs.ini and confUser.ini
When you install the game these files are installed in the root directory of the game (c:\program files\steam\steamapps\common\IL2 sturmovik cliffs of dover is the default path), but they are not the ones getting edited as you change settings.
What the game does is copy them over to the documents\1c softclub folder and it's this instance of the files that gets edited as you apply your settings: the ones in the root game folder are just the "blank reference sheets" that the game "photocopies" over to the documents\1c softclub folder for you to work on and save your settings and preferences to.
What you can do is force the game to rebuild the default files. First of all, back up these files from your 1c softclub folder and from your game root folder just in case. Also, go into the controls options and save your control layout for good measure. You need aero to be enabled for this in win7/vista because a windows pop-up will appear asking you where to save the resulting file.
The overlay window settings are ketp in confUser.ini so that's the one we need to fiddle with.
At this point, delete the confUser.ini files from the root game folder and from the documents\1c softclub folder, have Steam run a file integrity check and it will find the missing file and download it again for you.
The file will be placed in the root game folder (the "blank sheet"). Upon running the sim again, a copy of it will be created in the documents\1c softclub folder (where your actual edited settings go). At this point you should have the default overlay windows. See the sticky FAQ thread on the front page if you want to know more about how to customize them without manually editing the confUser.ini file
