I have not been able to replicate this behaviour. When i use DDU it removes everything including saved game profiles. I would recommend a fresh installation of Windows, as i think there might be an issue with your system.
Follow these steps:
Update Windows fully
Install one game
Create a game profile and then delete it
Do not install anything else for now.
Matt this is a fresh windows install and not an upgrade I just did it this week.
The crashes when deleting a profile seem random.
When Windows firsts installs it automatically load and installs an AMD driver and I have noticed that it will not install properly it pops up that there was an error installing the drivers. If you go into devices the drivers show they are not installed properly. Earlier builds of windows didn't do this so it may be a new thing.
My install is from a proper legit windows 10 iso so it was onto a clean drive too.
I do then go in and set windows not to automatically install graphics drivers after so I can install amd drivers from amd site, but you can't do it when you first install windows. There probs is a way to do it with an install script.
After trying several drivers and game profiles I find that all the uninstall programs including Amd uninstall program and the ddu from safemode and also using ccleaner do not get rid of some of the game profiles. Two profiles appear every time automatically one for Skyrim and one for skse which I never had on together.
I even tried going through the registry and deleting any reference to Amd. Windows must be storing some info for game profies somewhere else that the uninstall programs don't delete.
Installing the very latest beta causes windows not to display properly it has colours all over the screen and I have to reset my pc. One time it would not go away and I had to put my monitor connector into the motherboards connection and then reset and then switch it back which made the resolution go back to windows basic and I could then reset the resolution.
I always install drivers properly and never over the top of another one.
Something in the latest builds of windows 10 must be doing something with the Amd drivers and is making them unstable.
My other music pc running windows 10 with the same build, is running fine and works no problems with the gtx 680.
I have found that if I install radeon pro it does get the crossfire profiles to disable and skyrim does work much better even just having it running.
Uninstall radeon pro and create a normal game profile and crossfire does not turn off or it is not doing it properly I can't tell.
I do think that when you disable crossfire for a profile it does cause the clocks to drop down to 300mhz in fullscreen mode and fluctuate but it just isn't disabling crossfire properly. It seems the the gpu 2 goes hotter than gpu 1 but both cards get used. Usually when you disable crossfire it will be card 1 that gets used. Also clocks fluctuate if you use windowed mode again which is pointless we need the clocks to stay at full no matter how the game is displayed unless the game is capped at say 60fps and your card can get 60fps at a lower clock but its no good if it causes stutters or poor performance.
If you delete them and then press scan they come straight back.
Crossfire is defiantly broken in the crimson drivers. It is not working properly even using Radeon Pro in the latest beta fix.
I have now installed only the drivers of both 15.12 and 16.2.1 so no ccc panel and I tried using Radeon Pro.
Using radeon pro I can disable crossfire for a game in 15.12 but in 16.2.1 when you set crossfire to disabled card two's temperature starts going above card one on my r9 295x2 and it just doesn't seem like things are working correctly. Both cards have usage on them from time to time.
Normally when crossfire is disabled only card 1 has usage and the temp of card one goes up. Crossfire needs to be looked at properly as the r9 295x2 relies upon being able to either have crossfire working or being able to disable it properly for game profiles and the Amd software just isn't working.
Radeon pro also stops the clocks from fluctuating with out it the card is useless at the moment.
Using AMD own panel no profiles work at all, you can't disable crossfire for any game. I believe it is to do with the program not installing the profiles in the correct places or the ccc panel program simply doesn't work. As un-installing the software correctly does not delete the game profiles they re appear when installing the driver fresh so they must be getting stored somewhere else in windows 10.
I have a feeling it has been the 16. beta drivers that have caused this issue from a previous install and have installed it's software incorrectly in Windows or its game profiles are not being stored in the correct place so the program is not using them right. As windows 10 was fresh installed recently from a wiped drive it shows there are issues with the amd drivers and installs.