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This is an extremely poor choice of workflow that is unlikely to ever have successful results.

First, FXL, fixed-page EPUB, is a largely obsolete layout that has many problems. It's suitable only for 'picture page' books such as children's books and graphic novels, and should be used selectively even there. For anything like pages of text, it's the wrong choice, even though it seems to be a simpler option. For one thing, it's is very difficult to work with FXL EPUB after export, so it's a "you get what you get" format and resolving problems like this can be somewhere between very involved and impossible.

Next, placing PDFs in InDesign is a sort of specialized, niche way to get content to an end format. It is sometimes a good (technical) option, but going back to a live, source document instead gives more options for final output. And if you are indeed placing "pictures" on the pages, it again would be better to have basic graphics formats (JPEG, etc.) instead of PDF, simply because there are fewer steps in which export, settings, layout, etc. have to be considered and corrected.

Back up to original content (text or graphics) and lay that out as your InDeisgn pages; if you can, export as a reflowable EPUB instead of FXL. Any other path — working with PDF from a prior app, exporting to FXL, etc. — is going to be a headache and truly acceptable results may not be obtainable.