Thank you for sharing your experience.
Unfortunately, at the moment, you are hitting a known issue with iOS and the three-finger LiveSync. Upon application restart, changes are lost. To retrieve them, you need to do a three-finger refresh again on application start. Subsequent three-finger refresh gestures while the app is running should be getting your changes.
As for the complete rebuild, would you, please, be more specific? Does the three-finger refresh gesture not retrieve your changes? Which AppBuilder client are you using to develop your app? Is LiveSync enabled for the app?
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