Coming away from third party Identity Provider

Hi,

We currently have Office 365 and our Azure Directory sync is managed by a a third party service who do not use AD Connect but their own API. Once we configure ADFS our end and setup AD Connect will this break all the accounts on Azure since they have already been populated from our AD or will this re-enable the sync again once we come away from third party and allow SSO?

Also, would there be an issue with setting up AD Connect before we come away from our third party as Azure will be retrieving the same accounts from our ADFS and our third party identity provider?

Thanks,

Peter