I don’t have any problem with property value persistency with my custom components, so this seems to be a problem specific of your specific case.
I would investigate the error first. I have the feeling that fixing that error will allow the IDE to complete whatever it’s doing and fix the persistency problem.
Try to remove any code that is executed when changing any of your component properties, and see if the error keeps happening.
Chances are that the setter for property1 has a problem and raises the error, then the IDE stops processing your changes, and forgets about persisting property2. The problem could be in the setter of any property, or on anything that happens during the rendering of the component, which is triggered after any of the properties is edited.
You can use in_designer to avoid running code that would fail in the IDE.