There were actually 2 approaches to your problem
fix the filesystems on the emulated disks and rebuild.
fix the filesystems on the physical disks and New Config them back into the array.
I would have recommended 1, but since you had already started doing 2, I just went ahead with that.
It is still possible to do 1 if you want, and in some ways that would be more correct, Rebuild would recover any emulated writes, but since the filesystems were unmountable, it probably doesn't make much difference.