Is there any alternate way to be able to preserve the saves if user choose to ?
In NWJS export you can save game to a disk file. But if you need a cross-platform solution, then I think the only way is to use some cloud service like Playfab or Firebase.
I am currently using the save/load feature which is working fine, except that I am unable to clear or include a new save.
It's not possible to delete a saved slot. What you can do is use it in combination with Local Storage. Save a flag in Local Storage - "GameIsSaved=Yes/No". On start of your game load this flag, and if it's "No", then simply ignore the saved slot, don't load it.
Also I realized that if I publish new version of game with a different name for the save
Why do you change the save slot name? Unless you've made significant changes to the project, the old saved state should be compatible. With Local Storage you should also use the same key names when publishing a new version.