How can I add a file to a vault which is present on cloud?

I backed up an existing vault to pcloud and deleted it from my local system. Now I want to a add few audio files to a specific folder? How can I do this? Do I need to download the whole vault then decrypt it using cryptomator and then add the files?

Your vault files must be available on your local system. If your sync client does support files on demand, then the answer is „no“, because the client will only download when Cryptomator tries to actually decrypt a file (which is not necessary if you just want to add files).

Or you can use cyberduck if you do not want to have your vault local available and want to access it directly online.