dotfuscator publishing overwrite

dotfuscator CE

I am not sure of the exact procedure to ensure that my file is protected but here is what I tried in VS 2008 using vb.net.

1. Build final release
2. Open dotfuscator and build release .exe
3. Overwrite original .exe with one generated by dotfuscator
4. Open my project again and publish

However, it appears that the exe created in step 3 above is being changed again and thus losing my dotfuscator changes. :(

I also tried to publish first and to dotfuscator the .deploy exe but when I install this fails ...

Thanks in advance for suggestions. :)