Why were my fonts, margins, and spacing removed?

That's the formatter doing its job. A manuscript styled for writing (Times New Roman, double-spaced, one-inch margins) is not how a printed book looks. The Interior Formatter strips your Word styling and applies professional book typography — proper typeface, leading, margins, running heads, page numbers, chapter openers, and indents — sized to your trim.

What it keeps is your content and inline emphasis: your words, paragraph breaks, italics, and bold all carry through. What it replaces is the presentation: fonts, spacing, margins, and page geometry.

So don't spend time formatting in Word — it'll be overwritten. Give the tool clean structure (headings for chapters, normal paragraphs) and pick a book style here. See Which interior style should I choose?