How to recover progress that was unable to be saved in Undertale

If you're running the Steam version of the game, deleting files in the save directory won't be enough. Steam Cloud will automatically restore those files, and it also keeps a local cache of the files to restore them even if you're offline. While it's possible to clear these files out, it's complicated, and a simpler solution exists on Windows if you have sufficient access rights on your computer.

• Go to your computer's save location. (Default on Windows: [User folder]\AppData\Local\UNDERTALE)
• Right click the file system_information_962 or system_information_963, depending on if you are on post-genocide black screen, or post-genocide post-soul-sold.
• Go into properties, then security. Remove [Your username] and [administrators] rights to READ the file. Click apply.
• When you next start up the game, it will be as if you had never done a genocide run ever before.

If you're not playing the Steam version of the game, the simplest method to remove the consequences of completing a genocide run is to fully uninstall and reinstall the game.

Source: http://undertale.wikia.com/wiki/Genocide_Route#Consequence_Avoidance

There is no way in-game to view your progress percentage.

A good way to judge it is based on the number of areas in the game. There are 4 major areas in the game, and 6 bosses, all roughly evenly spaced. Using this, you can approximately figure out where you are in the game.