First, I am looking/planning to change this behavior in 0.6.
Second, you can disable the check/warning (temporarily) by clicking the red circle with a white line through it in the toolbar. Or under the quick settings menu item uncheck the well formed check entry. This will allow you to make all of your changes without being warned. As long you don't switch to book view while the document is well formed you will be fine. Switching to book view will force an automatic fix.
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