How to fix footnotes mixed into EPUB paragraphs
Check whether notes are inline, collected at a section end or linked. A consistent approach matters more than copying the original page-bottom position.
On this page
Identify where the note belongs
A footnote has at least two parts: a marker in the passage and the note associated with that marker. Find both in the PDF. Read the body sentence without the note inserted and confirm the argument still continues naturally. Then read the note separately. If the EPUB puts the note between two halves of the body sentence, the text may be complete but the sequence is wrong.
Keep markers and destinations together
When repairing a copy, preserve the note number or symbol and ensure it still refers to the correct note. A numbered list elsewhere in the chapter is not necessarily a note list. If the edition uses links, test the jump to the note and the return to the passage. If notes are placed after a section instead, check that their labels remain unambiguous.
Move a note without losing its reference
Match the note marker with the complete note in the source. Copy the EPUB before moving text. Keep the marker attached to its sentence and place the note in a separate, reachable location. If you add a link, test the outward destination and the return independently. Inspect neighbouring notes after the edit. A note is not disposable just because it interrupts prose.
These are targeted repair steps for your own file, not a newly executed before-and-after demonstration. Keep the unchanged original, an edit log and the exact reader version. Validate the saved copy and compare the full passage with the PDF before relying on the result.
Do not erase small text automatically
Small print may be a footnote, a citation, a table label or a meaningful qualification. Deleting everything below a font-size threshold can remove information the author expected you to read. When the note cannot be reliably associated, retain the PDF for that passage. A readable body paragraph is useful, but it should not hide the uncertainty around supporting notes.
A worked reading example
The note belongs to its marker, not halfway through the next sentence. Compare the complete body paragraph before deciding where to move the note, and preserve its reference number.
Check one note from end to end
Choose a marker in the middle of a paragraph, identify the full body sentence and locate the corresponding note in the source. In the reading edition, read the sentence first, then the note, then return to the next body sentence. The note may be presented differently from the printed page, but its association should remain clear.
If the note contains a qualification or citation you need, compare the exact text, including numbers and names. A footnote repair that restores flow but loses the note’s content is incomplete. Keep the PDF for formal reference work until you have checked the note and its relationship, not merely the surrounding paragraph.
Test the outward note link and return separately
Record the exact source marker and matching note. Open the note from the reading passage, check the note text, then use its return link where one is supplied. A correct outward destination does not prove the return destination is correct. Keep numbered markers associated with the right notes during repair, and inspect neighbouring notes after any change.
Inspect notes instead of inferring note accuracy
The reviewed paper result establishes checked scientific prose order, not successful footnote navigation. If notes are the reason for a new conversion, locate a marker and its actual note in your selected pages before proceeding. EPUBTurn does not edit the existing EPUB’s links. Preserve the original note and use a targeted editor when the defect is local.
If you try a new conversion, check whether notes interrupt the main paragraph.