Replacing file does not work

I tried copying a new version of a file over top of an old one in a
program directory under "Program Files" and it says the size is the
new size, but when I open the file in an editor it has the old
content. I even tried deleting the file first and it shows up as
deleted in the explorer window, but when I copy in the new file has
the old content.

I finally gave up on using Windows Explorer and opened the two files
in the editor and copied the contents of the new one into the old
one. That worked.

Anyone know what was happening to prevent the old file from actually
being deleted? I even went into the recycle bin and deleted the old
file there before copying in the new version. That also failed.