I have never seen a decryptor wipe an entire save ever... I have used 3 different decryptors since 2017 and they never ever gave me any troubles. Backups are always useful for a good reason, there's also the autosaves, or using a different save for making save edit, whichever works best for you.
Personal recommendation, you can use the sii decrypt for any format, it will be a tiny bit slower but at least you can use game format to 0 which prevents tiny spike lag during autosave from format 2.
If the problem persist, you could send me some screenshots. And maybe I can assist further on Discord too if you'd prefer.