After a bit of sleuthing, I've traced the problem to a corrupt abapp.wsp file. 

I will explain how I figured this out since the appbuilder docs is a bit lacking regarding these files. Both abapp.wsp 
and abapp.dfn are mostly ASCII 0's, but running strings on them shows that they contain dialog and window file names. 
The .dfn file also contains callback names. (So it's fortunate that this file was OK). 

To build the .wsp file, I created a new appbuilder project and in this new project I used the appbuilder UI to create 
dummy dialogs and windows for each of the respective files from the corrupt project. 

After saving the new project, I copied the /wgt/* files from the corrupt project over the new dummy files. This gave me 
a new project with all of my widget files, but missing callbacks. (Note that this step may not have been necessary - I 
didn't look at abapp.wsp after the dummy creation step).  

It wasn't clear how to proceed from here, but out of desperation I copied the new abapp.wsp file over the corrupt one 
and tried to load the corrupt project into appbuilder. Low and behold it worked.

Now I can run the appbuilder from eclipse and get back to work.