A week ago I made a save and it seemed to have no problems, but loading it back up resulted in all kinds of broken builds. Not sure what happened there, but if it happens to anyone else, I wrote a little utility (Sorry, I can't make Windows executables.) that should fix at least default bricks. It works in python 3.4, probably not 2.7.
Fixer utility:
https://github.com/paulguy/minitools/blob/master/fix_bl_save.pyYou'll also need:
https://github.com/paulguy/minitools/blob/master/BLSFile.pyIf you have everything set up, it should just be a drag and drop.
If anyone wants the original screwed up save to see what happened, I can provide it. I am curious to know how that happened.