ampfixer
Thankfully, good save and backup practices prevented any real loss of work, just 30 seconds of guitar. Ctrl-s is my best friend.

Careful and smart, Yoda is.

Being a client is sooooooooo much better than having a client.
 
I hope you get it sorted out John.

Really sounds like picture cash.

Cakewalk took a big step back in support when they removed phone support. There should at least be a "Pro" option for those making a living and willing to pay for it.

mentioned several times - clear your picture cache and see if that helps. sometimes (esp in earlier pre-X versions) i found SONAR "losing" the track but after reading someones comments on the picture cache, they came back as the project had to re-draw the waveforms. i think there is also a setting to set the size of the cache and you might expand it a bit in case there was an issue where the pictures were "rolling over" or indexing properly.
 
quick search result: http://forum.cakewalk.com/SOLVED-Picture-cache-waveforms-disappearing-in-large-project-m3479978.aspx
 

Hill62
Cakewalk took a big step back in support when they removed phone support. There should at least be a "Pro" option for those making a living and willing to pay for it.

Try obedia.com. They do remote desktop support, and when you need to have someone get your computer back online ASAP, it's worth the cost. I've used their support a couple times, and it was outstanding.

I used to loose audio clips in X3 and early Splat, recorded or dragged from browser. It turned out they somehow ended up 90 or 100 minutes down the project even though the song was 5-6 minutes long. So when audio is missing check content at the end of the project, you might be surprised where the end is.

I just upgraded my audio I/O to an RME UFX. That unit has a handy feature for situations like this. There's a USB port on the front panel. You can connect up a USB memory stick or USB hard drive and the unit will record a safety copy of audio. I don't do work for anyone but myself. But if I did do projects for others, I would definitely make use of that feature.

Afrodrum
I used to loose audio clips in X3 and early Splat, recorded or dragged from browser. It turned out they somehow ended up 90 or 100 minutes down the project even though the song was 5-6 minutes long. So when audio is missing check content at the end of the project, you might be surprised where the end is.

That would be if the "Always Import Broadcast Waves At Their Timestamp" option is checked.

ampfixer
While rebuilding the file I noticed that one clip was missing and two different clips had been given the same name.

This is the most important piece of the puzzle. The Bakers need to study what could have gone wrong there.