That, as I said, are store in a file named "persistent", in the same place than the saves files. If you have the save files, I don't see a single rational reason for the "persistent" file to not be there to, and to not store the needed information.
Okay, now I see a possible explanation. It's not that Ren'Py don't create the persistent file, it's that it silently refuse to load...
There's no way to help you with this.
Firstly, the tokens are unique for each computer ; what would be the interest if it wasn't the case ?
Secondly, the save files are unprotected, while the Persistent files are, and this will stay even with a fresh and correct "security-keys.txt" file.
Even restoring the file to its previous state more that surely wouldn't solve the issue you created without side effect. You need to delete all the persistent files (including the one directly in the "game/saves" directory), what will a small impact on the game, but not a breaking one for 99,99% of them, and hope that it will be enough.