You have to apply each license to each and every appliance, on top of that when you have a faulty license on a box, it is also stored on the SMO, so you need to remove every license that you need to delete with the g_cplic del <key> command, otherwise it will be back within 10 minutes.
For contractfiles I would expect the same goes there, also when a subscription is extended. On top of that when you use VSX and you want to use any of the blades, the VS0 need access to the internet to check on the contracts.
When you have an appliances that is not following the rules, for instance when you have VSX and 1 of the appliances has 2 licenses on it, one with and one without the VSX balde added, you cannot install any policy to that security group untill you resolve this issue, same for a license with any HA reference will not allow installation untill it is removed.
When one appliance has no license for a specific blade, to my knowledge it will just not work on that appliance.
Regards, Maarten