You can now export your Kobo highlights/annotations from side-loaded books to Readwise using a desktop app called October.
https://help.readwise.io/article/135...ghts-from-kobo
https://github.com/marcus-crane/october
Readwise is not a free service, but there is a trial. And once your highlights are in Readwise they can be exported to a number of other formats and applications, so you don't have to worry about your data disappearing overnight.
https://readwise.io/export
It's been working well for me so far.