I have been building my first theme on WordPress and have run into problem while adding content into different sections.
My HTML is somewhat like this,
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I've run into this issue several times now, and while the question is 3 years old, I think it's still rather current. I've succesfully used the Multiple Content Blocks plugin sometimes now:
https://ltz.wordpress.org/plugins/multiple-content-blocks/
After installing the plugin, you can just include the_block in your template: