After a little bit of reading/experimenting, I think this is probably caused by the Webkit2 no longer requiring a GtkScrolledWindow and handling scrolling on its own in a separate process. Whenever the existing scrollbar adjustments are read, the value is always zero, so the hack that was previously added for the old Webkit version no longer works.
A possible workaround might be to run some javascript in the webview that can read the scroll position and pass it back up to the plugin's C code so it's able to save and then other JS to restore it.