I gave up on Master Docs after about a month of testing them around 10-15 years ago. Too many problems, and I've never seen anyone say that they've improved since.
As Charles says, use Styles. They will make your life so much easier.
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5. Adding a table of content and a bibliography was pretty simple in the appended document.
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You know how the Headings Styles will automatically create an auto-updating ToC for you? Marry that with showing the Nav Pane for a simple way of getting around your doc.
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6. Simple drawings were prepared in Excel
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I have to guess that a simple drawing program would be better.
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each time I re-opened the Word-document the size of linked pictures was sometimes lost
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Did you save the pictures as separate files and use Insert to put them in the doc? Sounds like maybe not…
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the tool feature of Word is very versatile. Easy to change formatting and content afterwards
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Not sure what you're referring to with 'tool feature', but don't use the toolbar buttons for formatting—that road leads to the insane asylum
Use Styles.
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Make sure that you do not included too many lines with the Enter-key
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Do NOT use the Enter key anywhere in your document other than to create a new paragraph for content. Never for blank lines.
Btw blank lines do not work to provide breaks in ebooks—most reading devices discard them. You need a paragraph with some symbol like an asterisk for the break to show.