I think when you start to work with the openstudio application, you are actually adding some objects that the openstudio SketchUp plugin cannot interpret. It's better to finish your job with SketchUp and do the rest with Openstudio or EnergyPlus. But sometimes you forget to do something! In these cases, I would save a copy of SketchUp before starting my job with OpenStudio and EnergyPlus. If I need to add some objects with SketchUp later, I would go back to the copy that I have saved, make new changes, save the openstudio file, export an idf from openstudio, and finally copy the new objects from the exported idf to the main idf. If you intend to do all the simulations with openstudio I hope other guys can help you.

The most common operation that can cause errors is the use of undo. You can also keep the Ruby console open while you are modeling, if you do something that causes an error you will see a bunch of text pop up in the Ruby console. To open the Ruby console go to the menu item Window>Ruby Console.