Annotations belong to different layers
A PDF annotation may be attached to coordinates on a particular page. An EPUB highlight is often connected to a range of text that can move when you change font size. This is why a pen mark on a PDF behaves differently from a sentence highlight in a reflowable book.
Check where changes are stored
Some PDF apps save comments into the PDF file itself; others keep them in a separate local database. EPUB readers often store highlights in their own library data. Test with a copy before assuming your notes will appear in another app on another device.
Pick the right kind of note
Use page-based markup for diagrams, drawings and handwritten corrections on a PDF. For prose, highlighting a short quote and adding a typed explanation is often easier to review. When working on an assignment, include a page or chapter reference so you can locate the source again.
Export before changing tools
Look for PDF export with annotations flattened or retained, and for a notes export from an EPUB reader. Open the exported file elsewhere to verify that comments, highlighted text and the source reference are all included. A successful export notification alone does not prove the notes are portable.
Preserve the original document
Work on a duplicate when you plan to reorganize pages, convert formats or strip metadata. An edit that changes PDF page ordering may also make old references harder to follow.
If you mainly need to mark passages while reading, try a sample document in Readream Basic. Before relying on those marks elsewhere, check what your chosen file format and export workflow preserve.