My boss has an old computer with 95 upgrade installed that has gone corrupted after a bad shutdown and he had scandisk fix the files, over half of the drive was filled with .chk files and windows would not start.

I took a ride over with a boot disk with cd rom support made from my 98 machine to boot up and get cd rom going.
The first thing I did was delete.* chk to get rid of those chk files, they took up much of the drive anyway.
At the D: prompt I typed setup and installed windows over the original directory, when a file being copied is older than the source prompts came up, I chose to keep the existing files.
I left his house after the 1st reboot thinking he could finish on his own, but instead he told me the next morning Windows could not start because of a file. (he did'nt not the name of the file.) So I assumed that file was one of the newer existing files setup did not overwrite, so I gave him instructions to install 95 again, only this time to choose "no" when asked to keep existing files.
This morning he told me there was no change.

Now I'm beginning to think there could be a file that is outside of Windows that is preventing Windows to operate. I'm beginning to think I should format.
But can windows 95 upgrade be installed on a formatted disk the same way a 98 upgrade can?