That's just weird.
I have no idea how flex numbering would cause this, but I suspect you are still able to use hyper terminal for backup & restore? My only suggestion would be that if you ever have to completely reprogram the system manually, would WinDBAa work pior to changing the extension numbering?

[edit] Whoops, I see the DID numbering comment, etc. which assumes that it does work until performing the change?

- Dave S. -

You can never appease your ideologue opponents.