could be a problem with your hard drives. Are all hard drives formatted macosextended? Try running diskutility disk repair on all drives (you'll need to boot off a different drive to run it on your startup drive).
You might also try opening an autosave version of your project to see if that has maintained the connections.
And resetting your fcp preferences can never hurt
And here are some other troubleshooting steps
I have had massive hard drive problems with this project recently, 3 of 10 hard drives involved have failed. Perhaps that is another discussion item of how that could happen (24 hour operation for 3 months, I let them rest 3 days and they won't come back). What could have taken out so many drives all at the same time? Fortunately all are backed up. The missing files however do not come from the affected hard drives. All formated Mac OS Extended (Journaled). Some of the files it cannot find have additional copies on my main hard drive. Through the search function, it just does not see those files. I have to manually locate the files. This to me means there is some sort of corruption to the file search process. I assume it happens also when FCP needs to go look for the file during export.
The fcp project may have gotten corrupted.
That's why I suggested trying to open an autosave version. Have you tried this? Just find the appropiate job folder in the autosave folder and start opening recent versions (that predate the problem).
When you go thru the reconnect process, fcp usually says where it expects the file to be. Is the file still in the location?
I think its the computer. Two projects different projects with similar irratic symptoms. Its like it doesn't see some files, randomly scattered around several drives. I just got everything linked again and added a new external drive to export it to. 48 minutes into the export, the directory on the destination drive disappeared. I ejected the drive and took it to another Mac, drive appears fine.
One thing that occurs to me; Some drives have compatibility issues with other brand drives. Years ago I had a project, like yours, with media scattered over many firewire 800 drives. Had all sorts of issues before I discovered there was a compatibility issue between g-tech and lacie firewire drives.
Describe your setup and in particular your drive configuration. If you have multiple firewire drives connected, you might consider getting a firewire card for your macpro. They're not very expensive. Even though a macpro has multiple firewire ports, it has only one firewire bus. Adding a firewire card adds an additional bus. B and H photos has a few of these for around $ 50 or $ 60.