I have no idea either for twice update.
But the first rooted update.zip made serial/SKU = unknown, wifi ,e-ink can't be used.

second update solve the problem and keep suandr in /system/bin with root permission to execute (4755)

If you want to do any with system, do it with second update, no need to twice update again.

I would like to help robot but not for programming but design or debugging when there is problem, I have not enough free time during next 4 months.