Making a full backup will copy everything the way you have it right now, so yes, when you move into the bigger card all your games, apps, homebrews and roms will be the way you had them before.
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That's because the newest version of HENkaku spoofs the firmware but even Yifan said that is only a matter of time until Sony patches it again.
So it's better for people to use VitaUpdateBlocker and get to know it than use a temporary solution that will break in a few days and then wonder why it stopped working out of nowhere.