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I also use Skype, and i have not linked my skype account to microsoft, so my skype account is running the normal way as it was before without (it being merged with microsoft), hence the merger of Microsoft & Skype; gives the user choice what they wish to do.
If you link your skype to your microsoft account; The Microsoft email address you use to sign in to Skype with your Microsoft account will be shared between your accounts
No other personal or billing details are shared between your Skype and Microsoft accounts
When you sign in to or join Skype with your Microsoft account, your Skype contact list will include your Skype, Messenger and Facebook friends.
However, if you do not like it then you can unlink accounts and get back to how it was functioning previously.