I imported my manuscript and pressed "Regenerate all". Will it rewrite my own chapters?

Not unless you choose it. From version 1.9.21, on an imported book the "Regenerate all" window has an extra choice, "Your own chapters". It starts on "Keep them exactly as I wrote them", so only the chapters the AI added are written again. To have the AI rewrite your chapters too, pick a kind of rewrite there ("Rewrite from my text: polish", "...the book's style", "...expand", "...tighten", or write again from the chapter) and tick the box that confirms it. For an imported book, the window also starts on "In a copy of this book", so your original book stays untouched unless you change it. Your original text of every chapter is kept in its Versions panel as "Your original".