Updater.exe - This application could not be started when trying to update versions
As per the screenshot below:

Have you clicked yes? Any logs?
When I click Yes it just takes me to this page https://docs.microsoft.com/en-gb/dotnet/framework/install/application-not-started?version=(null)&processName=Updater.exe&platform=0009&osver=6&isServer=0&shimver=4.0.30319.0
Is there a log file somewhere that I can upload?
Got .NET 4.8 installed?
@Rem0o there are enough available SW maintenance tools / stores. I wouldn't put to much effort into a own solution. In my opinion users become more and more tired, to click updaters per app, instead of centralized solutions.
@Micke3rd.
The updater is literally 20 lines of code. It's a 1 click to update deal. Not much effort put into it. Supporting and maintaining different sw stores like winget, chocolatey or whatever will just add complexity imo. I prefer to maintain a single way to update the software, in this case being this github repo.
Supporting and maintaining different sw stores like winget, chocolatey or whatever will just add complexity imo
mhmm, that's also true
Got .NET 4.8 installed?
Yes its installed
Running the Updater.exe directly worked for me.
I just ran into this error as well, trying to upgrade from v121 to v127. If you look at OP's provided screenshot, the path to the program that is run is c:\windows\system32\updater.exe. I suspect recent versions of fan control are calling updater.exe without providing a path, and since the process is running with elevated privileges, the search path starts at c:\windows\system32, rather than the FanControl directory.
@Rem0o - is this plausible?