I’m not sure what you mean about ‘can’t download the newest Mono’; because I’m not sure when / what might be trying to download Mono.
When you switch Wine to a newer version, if the Wine developers have updated Mono or Gecko, Wine will show a popup asking if you want to download them. That happens when your version is outdated or missing.
002c:err:wineboot:process_run_key Error running cmd L"C:\windows\system32\winemenubuilder.exe -r" (126).
Thats tatally normal.
but not the latest vkd3d (there seems to be a problem with the download of this in bottles at the moment. I have 2.10.).
For your information, the current version is something like 2.14. But never mind, I don’t think this is related to the Directx3D implementation, wine or Mono if these things did not help. I just wanted to know if everything was up to date, because always is possibility that could help.
Wine is far from perfect and sometimes things just break—sometimes because of a system update, sometimes because of a Bottles update, sometimes due to changes in the prefix settings, game update or just bug in wine causing data corruption.
You’re in a good position since reinstalling actually helped you. That’s not always the case. Sometimes you need to wait months—or even years—for regressions to be fixed.
Appendix
I don’t know how familiar you are with Wine, but for the future remember: dxvk is not the default Wine implementation for DirectX 9–11. By default Wine uses wined3d, which is slower but often more robust. So if something doesn’t work, just try disabling dxvk.
However, in Bottles there’s currently a bug (I think) where to switch properly you first need to change the Wine version to an older one, and then back to the version you actually want to use.
It’s best to enable performance monitoring and check whether the game is running with dxvk, vkd3d, or wined3d to be sure.