If you accidentally delete a file, you should be able to restore it from your backup. If you work locally in your vault, and it is immediately synchronized to your cloud storage (mirror sync), then the vault is not a backup. A backup contains data regardless of the current state of your local work files (basically). Just to restore a previous state if necessary.
A backup process does NOT delete the files when they are deleted in the data source. The sync process of your cloud provider does exactly this (delete files online if they are deleted local) and is therefore NOT a suitable backup solution.
Cryptomator itself is not a data availability solution, but a privacy protection solution for files stored online.
If you want to prevent data loss (e.g. accidental deletion, or hardware failure, or malicious attack), then you need a backup solution.
Here’s an example setup:
Work Folder: D:\ (encrypted or not but not synced to your cloud storage if not encrypted)
Use a backup solution to backup files frequently to your backup destination X:\ (X is can be a vault). Configure the backup solution to keep file versions (depend on your needs, in my case I keep 5 File versions when modified and one permanently when deleted in the source).
If your Backup Folder X is a vault you want to have stored online too, make sure the vault files are placed somewhere where the are included into the sync operation of your cloud providers client.
Now, lets assume you deleted a files in your working folder D:. Then open your Vault X:\ and restore the File-Version you want to restore.
As you can see: the backup process itself does not rely on cryptomator. If you want to store your backup online and keep data private, you should backup into a cryptomator vault.
Maybe you are interested in reading this: https://www.techsoup.org/support/articles-and-how-tos/your-organizations-backup-strategy