It absolutely is another program, I can tell this because it has a different name. To run it I type "nvim" instead of "vim". I use different config files to control its behavior. I install a different package on my system when I want to use it on a new computer.

If it really is another program with reference to vim, it should leave undo files made by vim alone.

If it's going to nuke vim's undo files, it can't hide behind "another program".