If the file Conquer is defect (by some pvper who thinks he is funny posting some non-working app for example), you should do the following:
1) Open <CO2-directory>\version.dat in notepad or a hex editor or whatever and change the value to 4311 (well this is untill the next large update).
2) Now start AutoPatch.exe.
3) A "patch" will be downloaded and all files will be extracted on the right places, overwriting your corrupt versions.
MIND: Not all files will be recovered, so your client may still not function as it should, but it is a start, and you can try this to not have to redownload the whole game.
I know this is not too usefull and most of you will know this, but I fixed it and I thought: "Let's make this a post ^^"