I think I've figured out how to duplicate:
1) create and save a project proj1.rpp (creates new .rpp-undo)
2) make some mods, save as proj2.rpp (creates new .rpp-undo)
3) make some more mods, save as proj1.rpp again -- incrementally updates .rpp-undo, incorrectly (needs to full write it).
FIxing this, thanks!