Although I never used it, I am aware that Calibre can serve books in your local network. I imagine that this offers some position and annotation sync.

Also, a bit off-topic for this sub, but… how do you read? E-readers? Tablets? Software choices?

Unfortunately, there was never great ebook hardware. I use a tablet with Android. KOReader for ePub, constantly trying new Android PDF readers but finding nothing decent.

While not intentionally, running Syncthing between all my computers means that my PDF annotations get synced across devices. ePub ones do not; afaik KOReader uses its own metadata format that it stores as a standalone file.

Before, when I was still in university, I used Zotero also for annotation management. Feels like an overkill nowadays since I only read for leisure.

I use Calibre to store and manage my library, and then serve it to KOReader clients on four devices. There are two ways to serve books from Calibre to KOReader but I prefer the "content server" approach where Calibre runs a server that I can browse from within KOReader. (The other approach, "wireless device connection," lets KOReader show up as a device you can drag-and-drop books to from within Calibre, but comes with limitations.)

When I start a new book I manually download it to each device and let KOReader's progress sync plugin store my reading progress across devices. Highlights and bookmarks don't sync between devices, but there's cross-platform desktop software called KoHighlights that I use to merge my highlights when I'm done reading a book, then I keep the merged version on my desktop KOReader library and delete the book from my other three devices. Other options for long-term storage would be using KOHighlights to export the merged highlights to plain text, HTML, CSV or Markdown, or using KOReader's built-in functionality to export notes to a Joplin notebook (or a number of other formats). I know there's also a way to send the highlights back to Calibre, and I did get this working at some point, but I remember it either being hassle or not working well.

KOReader also has a way of saving highlights directly into PDFs (and only PDF files, I believe), and I think this is the default, but it's something I've disabled.

after ~~reading~~ hearing of studies that came to the conclusion that highlighting and adding notes is for nothing, I try to form the habit to summerize thoughts in my own words; and for fiction books write a short review after reading it.

I've written a hacky Bash script that exports my kindle notes and highlights of selected books as a text file. By default kindle lumps everything in one file and it's such a mess

Not a perfect fit but Firefox can annotate PDFs out of the box. Maybe in some cases that is helpful ?

Jailbroken Amazon Kindle Paperwhite 2 with Koreader installed. Never really bothered to take notes while reading (let alone sync them), so I'm gonna follow this thread.

I download my books from Soulseek and manage/transfer them using Calibre.