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Like spinnerlys said, use Apple+0 to open up your new good timeline settings. Write down every setting that you see in that first window. Close it and open your edited timeline using Apple+0. Make all these settings match your new sequence and your edited one should work properly.

As far as the export use quicktime movie to keep it in prores at full quality. If you want to change the format to something other than your fullres prores, use the quicktime conversion.
 
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