FreePBX loses file content, Upgrade gets hosed

Yesterday our FreePBX 2.9.0.12 suddenly stopped routing inbound and outbound calls from our T1 line. Asterisk was working. Our Digium T1 card had a green light. We have support from Digium and they looked at the system and determined that the calls were coming in but could no longer be routed as the entensions.conf file from FreePBX was missing code on how to route the calls. Internal calls were working. The GUI looked normal. At this point Digium said they could no longer help us because it was a FreePBX issue. It appeared to be a bug.
This morning I looked at the FreePBX site and saw that version 2.10 was out and did a backup of the system then did the 2.10 upgrade on the Framework module.
This script stalled and sat there. I can now log into FreePBX. It says that I have 41 module updates but I get a Fatal Error when I check for updates to upgrade the remaining modules. At this point when I try to go around the GUI it asks for the username and password every time I change to a different item.
I was hoping that by upgrading to the latest version it might correct the original issue. Now it looks like this install got hosed by FreePBX. Anyone have susggestions?

You did not mention how you installed the original system. It sounds like a PHP issue.

Impossible to tell without more information.

You did not mention how you installed the original system. It sounds like a PHP issue.

Impossible to tell without more information.

I played with this yesterday and was finally able to get the GUI working again. I also updated the additional modules after the Framework. This morning I tried testing the system and none of the calls are routing. External calls coming into the system receive an error from the Telco saying this number is unavailable.
So, upgrading did not seem to fix the issue. My inbound and outbound trunks are listed in the GUI. All my extensions are also listed. I don’t know how the file would be missing code if no one made changes and applied them. If this is a bug in FreePBX do I still have to pay for support to fix their problem?

I don’t even understand your question about paying. If you want support from the support team you have to pay for it.

If you find a bug in FreePBX by all means report it. The dev’s fix bugs fast.

You haven’t done any troubleshooting so I am not sure why you would think it is a bug.

I mean what does the log show when the call comes in? What about dialplan show commands in Asterisk for the dial pattern?

Is everything included properly in extensions.conf

Are the ownerships set right on the files.

Or, as you said you could pay FreePBX supported and be back up in a jiffy.