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Pretty print tidy doesn't usually cause too much trouble. HTML tidy can be a real problem.
The HTML tidy problem can show up mostly in the event you do lots of text mangling with search and replace. It can eliminate whole paragraphs or skipped words and if you are not really good at proofreading, it can slip out and the reader catches it. Automatic repairs can be in this category too.
In your position writing the stuff in the first place, you know how it is supposed to go. But it can be like highway hypnosis... you know how is supposed to go so you see what ought to be there, especially after the 17th revision of the scene.
If you going to run on automatic you might consider text to speech to read it back to you and save save save.
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