We’ve bumped into this issue with Sync Center for clients with employees who often work from home several times recently.
A user selects a folder or two in a shared drive for offline use. Then, when they connect over the VPN, or sometimes even on the LAN, they can only see the folders they have synced and the rest have a gray “X” on them.
It has to do with windows thinking it is on a slow network connection and kicking the drive to work offline mode. You see how this would make sense over a VPN? :) So, in group policy, there is actually a setting to disable this slow speed stuff, even though it is not configured by default, it is still applying the default and you need to go in and disable to get sync center to work right over a VPN.
“Computer Configuration > Policies > Administrative Templates > Network > Offline Files > Configure slow-link mode” and the second one we disabled is the link speed. shouldn’t matter, but we disabled it for good measure.
This may not always be the answer, but in the most recent case, as soon as we applied it and ran gpupdate we tested and the problem disappeared. They even disconnected/reconnected the VPN numerous times and every time the full drive came back!