If the user is removed from LDAP, then user doesn't exist in Splunk (hence the CLI command remove user won't work). The error that you're seeing is for the Splunk knowledge objects (searches/dashboards/macros etc) owned by that deleted user. To fix the errors, you would need to
1. Delete those objects (if they are no longer needed)
2. Change the ownership to a different person (same team member/replacement)
3. Change the ownership to nobody (you would need to update the scope from private to this app.