Hi @tsme
If you have a scheduled config or operational backup then ISE will attempt to authenticate to that sftp repository at the configured interval (e.g. daily, weekly, etc.).
If you configured the repo credentials in the GUI then it should replicate to all the nodes in the deployment (as you stated).
If I were you I would SSH to each node's CLI and issue the command
show repository <repo_name>
to check whether the command works - if it works then you should see the directory contents. Do it on BOTH nodes. Perhaps one of the nodes has an issue because password didn't replicate. And also check that you have the crypto keys on both nodes.
Command :
show crypto host_keys