When you "lost all of the I/O attached" was the T1H-EBC100 happy? Or unhappy (error lights)? If it was happy, then a bad connection in the base modules may have caused it to power up not seeing ANY I/O at all and it was ignorantly happy about that. If it was unhappy, then on power up it saw the modules, logged them in, and then at some point they logged out. This would've caused the T1H-EBC100 to be unhappy (error light).
As far as your logging them back in procedure... I don't have any idea what was really going on there. Very odd.