You cannot manage App-V client using both Sccm and Appv Server. In your scenario, may be when you have published through SCCM, it would have removed the appv publishing server from the client end.
As long as package is not published from the SCCM, it might co-exist (Not Ideal case)
To know more check this KB article -
https://support.microsoft.com/en-us/kb/2780808
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