The original problem could be a known issue when creating bond including the management interface that we have to investigate. Although the emergency network reset should have fixed that, so maybe it is a mix of the bond creation issue and MTU issue.
In the reinstalled pool, did you create the bonds already? If so I would think changing the MTU should be fine, especially as it worked on other PIF, but with MTU issue it is often quite sneaky, so I would not make any promises either.