Have a client that didn't report any troubles or notice any problems but simply wanted to add a new extension for a new hire along with a new phone. Figured piece of cake so went into comm closet and noticed the SL1100 unit flashing blue followed by red. I logged in with PCPro and found that the system was not seeing one of the extension/co cards. So in programming, I can't see anything below extension 113. But yet extension 101 and those below 113 are working but can't be updated.
Any ideas?

A power cycle reboot clears up some of the odd things in the 1100.

That's what I thought. After I added the extension, I power cycled the main unit and at first I thought it cleared but red light came back after it completely booted up.

Red alarm light has to be cleared via phone programming

In the manual page 2-598 Program 90-53-01

I believe.

You do have to clear alarms thru phone programming. The reboot might help with being able to see the missing extensions.