The confusion is that the first two options deal with how to handle the old config files and the third option is what to do with the .new files.

The options should all be with respect to one perspective, preferably the .new files because that's what's changing.

There is technically nothing wrong with the current prompt because it functions as it is described.

However

There is intuitive design and obtuse design. Both facilitate certain responses. If you purposefully make something obtuse, you force the reader to actually comprehend what they are doing before performing an action. Thankfully, the user will always end up with a copy of their old configure files either being used or backed up.