When I saved a ship with reactor size level 11 that had a defensive chamber chain of Shield Capacity 1 and spawned the ship in again the following glitch occurred:
Half of the defensive chambers on the first level remained active, however the other half had been changed to deactive. As a result of this the first chamber was marked as invalid and only containing 50 blocks. In order to fix this I needed to remove the first chamber in the chain, then replace it.
I am unsure if this is a bug related to chamber chains in general, or only to the shield chamber chain. It is worth noting that a similar glitch may have occurred when I experimented with the FTL Chamber Chain, however that is a topic for a separate bug report.