Hello @Cloud_Geek_82
Thank you for reaching out. Ideal fix for this would be to remove user from Azure AD as well, however this would remove the Mailbox and other associated data on the account from Azure AD and Exchange as well. The workaround I can suggest you is to identify the affected object and set its Immutable ID parameter to Null. Doing this it would remove any reference to its linked AD Object.
Command to check if the Cloud-Only affected user has ImmutableID associated with it.
Get-AzureADUser -ObjectID "Affected User's ObjectID" | Select-Object -Property UserPrincipalName,ObjectId,ImmutableId,DirSyncEnabled
Command to set Cloud-Only affected user has ImmutableID to $Null
Set-AzureADUser -ObjectID "Affected User's ObjectID" -ImmutableId $Null
Once this is done perform a delta sync on Azure AD Connect and the error should be removed.
I hope this helps and hence would request you to please "Accept the answer" if the information helped you. This will help us and others in the community as well.