Compile messed up

I’ve written a short family history with a dozen photos… It looks fine before Compile. But I mistakenly I guess started out w non-fiction template. Someone is asking for a pdf and so I compiled pdf and I had no chaps just 2 parts but now it’s messed up. Can I start over with no template and just compile a simple outline? Do I have to start a new project and copy paste into it?

Look at how you assigned section types is often the first area of problems. You can also make a collection of what you to compile and in the third panel can in the dropdown area choose to just compile the collection. Test this out and see where there are issues. If one section in particular is a problem, consider using the As Is Section Layout. Remember Section Layouts can be modified to change how the compiled product works.
Section Types are a label attached to documents to funnel them into Section Layouts which control how the output looks.

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I think I’ve worked out the section type problem. All the paragraph indents are inconsistent. Is there any way to fix that before compiling?

Take one file and set your paragraph indent and formatting just the way you want. ( no tab indents) . Then go to project settings and click inside the file to set it as your default format. Now select everything in manuscript and on the beach but believe is windows> convert> to default formatting. Consider making a backup before doing this in case some thing gets messed up. I hope that works for you.

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