You can not encrypt existing online Data with a local encryption (cryptomator) without having the data local.
That means, if you want to encrypt your existing data, you’ll have to download it (if not already available local), encrypt it and upload (sync) it again to your cloud storage.
Cryptomator desktop creates encrypted files local, that are synced via your storage providers client to the storage. Cryptomator is designed so that your provider never has access to unencrypted data.
Maybe this tutorial will interest you, or you might want to have a look at the Documentation:
