Deleting the project and starting again was very much the wrong thing to do. What you describe is almost certainly not an issue with Visual Studio but with your own code. You most likely have build errors so when you attempt to run your project, it fails to build and then an old version of the EXE from the last successful build is what runs. When the build fails, the default behaviour is for VS to prompt you whether to run the last successful build output and it is possible at that point to say yes and to tell VS to do so without prompting in future. It's quite possible that that's what you did and now your code just keeps failing to build and you keep running the old output.
You should pay attention when you build - that happens automatically if you change the code and then run the project - to see whether it is successful or not. You should also open the Error List window to se if any build errors are listed there. You can also delete the bin and obj folders from the project folder so that no old output remains and then you cannot possibly run that output without intending to, so you'll know for sure whether your build is failing.
If what I described is not the case then what you're seeing is not normal behaviour and your VS installation is broken. There's no switch to throw to unbreak it. You need to fix it. That's exactly why the VS installer provides a Repair option, which is basically a reinstall in place, as opposed to separate uninstall and reinstall operations, which would require you to select all the installation options again. If the issue is not your code but the IDE, that is what you should do.