Short answer: The highlights are saved in the Clipboard folder inside the app’s folder.
KOReader is an e-book viewer that can be installed on e-readers like PocketBook and other e-ink devices. The application can also be installed on Android and Linux computers, where it’s commonplace to find e-book viewers that support exporting highlights, notes and other annotations.
Fortunately, KOReader supports this useful feature too, which you can find under Menu > Wrench / Spanner icon > Export Highlights
KOReader can open several document formats, including the most common — EPUB and PDF. The viewer supports highlighting in both formats however, unlike PDF, the EPUB format does not support saving / embedding the highlights within the file itself.
This is a limitation of the EPUB format and not that of KOReader. Indeed, finding viewers that can highlight EPUB is a rarity even on Windows and Linux which have access to numerous e-book viewers.
With the PDF format on the other hand, annotations are saved within the file itself and thus can be viewed on other devices and e-book viewers. Nevertheless, programs like PDF-XChange do support exporting highlights from PDFs into separate PDF files or other formats such as Plain Text, HTML or RTF.
Consequently, it’s necessary to export highlights from formats like EPUB and Mobi that don’t natively support embedding annotations. In the case of KOReader, the highlights for e-books are saved in a separate database. This also applies to PDF files up until when you manually save the document by using the Save document (write highlights into PDF) option under Menu > Gear icon > Document.
Once exported, you can access the highlighted files by going to KOReader’s installation folder in your e-reader and checking inside the Clipboard folder.
For instance, in a PocketBook like my Touch Lux 5 the full path to the folder is as follows: Internal storage > applications > koreader > clipboard
The default folder for the exported highlights on Android is the koreader folder in the root of the internal storage as follows: internal storage > koreader > clipboard. If you need the full path, it’s:
/storage/emulated/0/koreader/clipboard. On Android, however, it is possible to change this folder to one of your choosing.
KOReader saves the exported highlights in two formats — HTML and TXT. You can transfer them to a different folder in your e-reader for easier access, or better yet sync them to the cloud or save them on your computer for safekeeping.