Missing Files in ColdFusion-based Flex Projects

This one threw me for a loop. I'm documenting it here so I'll remember the next time it happens.

I was working on the TorontoFlex user group application, which is ColdFusion-based. The application is architected as follows:

The main file is index.mxml, so when I compile, I get index.swf and index.html (and other files), which I deploy to our ISP. I tend to manually build projects in Flex Builder so that I don't have to wait on every save. At one point I did a "Build-all". All of a sudden, the index.swf and index.html were gone! Also missing were the supporting files, history.htm, etc.

The problem? I had an error in my code, and had the Problems tab set to only show errors in the current file. Before I realized this, I tried compiling on the command line, where I saw the syntax error I had introduced. As soon as I fixed the error and re-compiled, the files magically re-appeared.

Admittedly, the problem was my fault, but deleting files?! I haven't tested this under Flex Builder 3 beta, but I hope it's dealt with a little more gracefully.