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I locate chapters in separate files, as shown below (a book of 500 pages, 14 chapters).
The document class is based on the book class:



To speed up work, I compile chapters separately by, for example:


I organize a chapter's floats (by moving text around), one chapter at a time. When I then finally compile all chapters together, the floats move from where they were before. It is as if previous chapters' floats affect later chapters' floats - some form of float memory across chapter boundaries.

I realize that \chapter forces a \clearpage, and tried \afterpage{\clearpage} and \FloatBarrier, but with no effect.

Is there a way to better isolate the floats in chapters from each other?

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If you process the separate chapters in order then you should get the same behaviour as if you process without \includeonly. As you comment, \include uses \clearpage at the include boundaries so no floats from one chapter will affect others. However the position of floats can in delicate cases depend on the text in the rest of the page. Notably \ref and \pageref can produce different numbers or ?? if chapters are processed out of order, or not enough times. As this affects the length of the text it can affect line breaking, and so page breaking and float positions.

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