Commit 11d39910506bd5fc52a76e43ed4f3cd99bae48e0 started clearing the whole DirectX keys before filling in the devices with info. I missed that there are some values set on the key itself in wine.inf.in (Version , InstalledVersion), those can also be modified, by, e. g., native DirectX installer.
I think it is best to just delete the subkeys and leave the values untouched. Those subkeys are only device guids on Windows which we refill anyway.
Thanks @tclem for pointing that out.