Upload the difference of changed files instead of the whole thing

I'm using RClone to sync my eBooks directory with my Google Drive. Every time there's a change in PDF annotations and the file changes slightly, RClone uploads the whole file all over and replaces the old file.

I wonder if there's already a relevant feature to address this issue or if it needs to be implemented.

There is not and most likely will never be for direct operations like sync. The reason is that most cloud storages do not provide such functionality - update only part of a stored object.

So in general for rclone sync you are out of luck. However if what you require is a backup you can check backup programs like restic/kopia etc.. They allow it by splitting files into chunks stored as separate objects.

In theory rclone chunker overlay could provide something similar but I do not think it is something anybody is working on.