I think you contradict yourself, since EXTERNAL memory is emmc (hence the "e" I guess).
It could be Odin that wiped the internal sd? I said that because I just restock just 2 min ago using heimdall and my internal and external sd are intact.
About restock requirement, I am not so sure also about CM9 because I am on AOKP.
But many have confirmed on AOKP that we don't have to restock, just need to flash Overcome Kernel.
With that, the MTD converter will detect that your "machine" P1000 and will proceed to convert. Some sort of fail-safe mechanism.
HumberOS mentioned that if you are on one of his ICS kernel, the machine name will not be P1000, don't quote me, but I vaguely remember that he said it is mach-p1
So, if you want to shortcut, try just flash Overcome Kernel 4.0 and boot to recovery and flash your latest CM9 MTD