I have had this happen twice to me and I'm not sure how to reproduce it since it occurs randomly.
I have several jBPM projects set up in Eclipse. I can open and close the projects fine. I can also close Eclipse and reopen it and usually my projects reappear.
One day I attempted to open Eclipse and the references to all jBPM libraries were gone. The jBPM library still existed in the Libraries for the build path but the jar files associated with it were gone. Has anyone run into this before and if so do you have a resolution.