HOI2 and DD have an executable with the same name : hoi2.exe.
So when the patch check the registry, it use the first one found that is in the first disk listed :
if HOI II is installed in disk G and DD in disk C, then the patch will apply correctly.
if DD is installed in disk D and HOI2 in disk C, then the patch will apply in HOI II, and by so make HOI 2 unplayable and DD will be not updated.
That is an old issue that I did already addresses to Johan the very first hours the patch 1.1 was released and I got the answer : it's difficult, we are working on it. If after some month the issue isstill existing I do presume it must be uttermost difficult to fix it (kidding but humor is a way to evacuate bad feelings).
By so, and it's the resultant of what I said, if you have on the same computer HOI 2 and DD, and UNINSTALL hoi2, ALL accurence of hoi2.exe inside the registry will be deleted, even if they belongs to DD and not to HOI2. The answer I also get to that problem was the same : too much complicate, we are working on, uninstall HOI2 and DD, clean the registry manually, reinstall ONLY DD, apply patch and then reinstall HOI2 , apply patch, then go to reinstall Cpack icon, GIP, story road ... .... .... .... ... .... ...
So , too make it short, the problem is well know by at least Johann and 2 other members of PI team, I also addressed them some possible workaround (mods to do the patch to make it apply correctly), they simply do not have the time to do it right now I suppose. But it will certainly be fixed in 1.5 or 1.9, at least I hope.