This question does not appear to be a Skyline question. If OP has not already reposted to the vCenter Server section, I advise doing so. VMware GSS will advise you that vCenter Server versions needs to at least match the level of the hosts. Also, in case you did not know all builds of vSphere 6 are no longer supported. This may play into your issue.
If the questions is truly related to Skyline accessing the upgraded vCenter Server, I have found that this happens due to a change in Machine Cert within the vCenter Server. To address this issue, login to your Skyline collector and find the configuration for your vCenter Server. Edit the configuration and if my guess is correct, you will be prompted to accept the new certificate. Once you accept it, allow a few minutes for systems to sync up.