I have noticed new behaviour of re-appearing contacts: all contacts from 'Skype Contacts' subfolder in Outlook.com has been automatically deleted and moved to Trash folder. New Skype contacts (added in Skype recently) appear for some time in Outlook.com
contacts, but after a couple of minutes move to Trash folder; 'Skype Contacts' subfolder disappears after that. Moreover, some old Skype contacts still re-appearing from time to time in Outlook.com contacts (with recreation of 'Skype Contacts' subfolder) and
moving after short period of time to Trash folder (with subsequent disappearing of 'Skype Contacts' subfolder).
I've also managed to delete my empty 'Google Contacts', 'Exchange Contacts' and 'Facebook Contacts' subfolders from Outlook.com via Microsoft Outlook desktop application (it wasn't possible before).