IIRC Kindle will always do a full screen refresh in 3 cases:
1) page / screen had an image displayed
2) after showing then hiding part of GUI (things like top bar with icon, main menu...)
3) since you're using PDF there is lots of scrolling and zooming and those actions will always trigger a refresh
So probably the PDF you're reading is "images based" (= scanned pages, 1 page = 1 image) instead of text PDF?
Anyways there is nothing you can do on stock Kindle software to stop that. If your Kindle is jailbroken you could test KOreader and check if it will be any different when dealing with image based PDF. KOreader is in general much better for reading PDFs and among other things it offers more granular control of how often you want a full page refresh... similarly to Kobo readers.
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