This has happened to me at least twice, and I've yet to figure out what the cause is. I tried searching the bug DB and didn't find any prior reports of this, but it was hard to formulate search terms that would provide accurate results. If it's a dupe, sorry.

The issue is, I open the Configuration page for a job that has a shell script configured as a build step, and the contents of the shell script text box is blank! The config.xml for the job shows:

<builders>
<hudson.tasks.Shell>
<command></command>
</hudson.tasks.Shell>
</builders>

This is a horrible data loss bug... I've had to reconstruct the shell script by looking at the console log of previous job runs. Furthermore, the job still "succeeds" because the various other build tasks work, so you might not immediately realize that it wasn't doing everything it was supposed to!

If there's anything I can do to increase logging on my side or something to help track this down, please let me know. For now I'm going to start making hot copies of the job config.xml files every so often so I can recover the configuration if need be.