Here's a nasty bug in the new WO Builder I found yesterday:
If you set your default encoding in WO Builder for WebObjects 5.3, then open a component, you'll first get an error saying that WO Builder doesn't understand "Unicode (UTF-8)" or whatever encoding you chose. Then, if you make any changes to your file and save, it will rename your component to your component name with a ~ at the end. e.g. MyComponent.wo~. Oh, and WO Builder will still have the dirty bit set in the red dot in the title bar. Thinking that WO Builder didn't save your changes, you save again. WO Builder will then delete the MyComponent.wo~ directory. There's no MyComponent.wo or MyComponent.wo~ anymore. Your component has been completely deleted.
I sat down with a WebObjects engineer at WWDC and showed him the problem, so they're aware of it. Guido Neitzer (sp?) was there with me at the time and he also was able to reproduce the problem and show the WO engineer.
Fortunately, there is a workaround. DON'T SET YOUR ENCODING in WO Builder preferences. Leave it at "NSMacOSRomanStringEncoding". If you've already done this, then quit WO Builder, open Terminal, then execute the following command:
defaults delete com.apple.WebObjectsBuilder DefaultEncoding
Then you can safely save your WO components. It even carries forward your .svn directory after it creates and deletes the ~ backup component.
I've had the same problem, too. See my last post.