Uninstall.exe = NUKE.. Recommendations?

I assume the only way to uninstall without using the uninstall.exe is to delete the files individually. Does anyone have a picture of the folder/file structure of a fresh install or any other recommendations for me? Explanation below.

I accidentally installed RetroArch directly in the Program Files (x86) folder resulting in the folders and files mixing with all my other program folders and files. Upon running the uninstall.exe to fix it, it began deleting absolutely everything in the x86 folder and I caught it after it had deleted 300GB worth of data… I was able to recover and replace roughly 260GB with the rest recovered but displaced from where it goes so essentially lost. I am still however left with the issue, I have RetroArch files and folders spread all over in the x86 folder and I don’t know which ones are RetroArch files.