There are some links in my original PDF files and of course I need to retain them after imported to flip book. But the fact is no links available in flash book. I can’t keep links in original files? Do I have to add them again manually?

No you don’t need to add them again.
In the “Add file” window, don’t hurry to click “import now” button. Make sure the “Import links” option was checked if you have links to import.

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