Multiple certificates with HttpClient
While not really directly answering how to deal with your certificate issue, I would suggest you a workaround that would work even better.
Use the OAuth authorization with Bearer token and Azure AD authentication for the Service API, instead of the certificates.
Thus, instead of managing multiple certificates, you would just use ADAL to get a token from the Azure AD. And the single token you receive will be valid for all the subscriptions the user has access to.
You can read more on authenticating service management API calls with Azure AD here.
And you can learn more about using ADAL with Windows Phone app here.
You grant your native client application access to Azure Service Management API:
