My way - bullet proof.
1st - Copy the game folder contend from SteamApps\common\ for a new folder(example):
D:\Cliffs of Dover
2nd - Execute the "TF 3.00 Mod Installer.exe" - point this new folder.
After done the first patch install run through the Laucnher.exe in this new folder briefly a QM to check is OK.
Then delete the contend from:
:\Users\(user name)\Documents\1C SoftClub\il-2 sturmovik cliffs of dover - MOD\
cacheInstall the second patch, repeat the same process.
Install the third, repeat the same process.
Install the fourth - this one is advisable extract the 2 files for a temporary folder first, due size:
Mod 4.0 Installer.exe
Mod-v40.zip
Run the "Mod 4.0 Installer.exe".
Repeat the same process above. If all OK make a shortcut for the Launcher.exe and place in desktop, etc.
In this way, you have a backup of "original" inside STEAM folders, case need reinstall TF Patchs for some reason.
Will run CloD outside STEAM and thus avoid the common issues with STEAM Cloud, lost controls (joy/keyboard) configurations.
Or, if prefer, skip the 1st steep and do the rest, installing over the STEAM copy.