For some reason when I save files in WinSCP, it reverts the owner/group back to root. Is there a reason why this is happening? It only started happening recently. I am not sure if this is a WinSCP problem or a server problem.
WinSCP by default, transfers files larger than 100 KB to a temporary file first, renaming them to a target name only after a transfer finishes.
This has some advantages. But also the disadvantage you are facing, ownership of an original file is lost.
You can disable the behavior in WinSCP preferences.