There might be an easy way to move away from eBooks without losing your annotations.
I’ve never used a Kindle, so not sure whether the My Clippings.txt file contains (all) Kindle annotations or what kinds of annotations Kindle offers at all.
If you used highlight annotations then this file should contain all of them (as far as I know) - and if you have a PDF version of the eBook then you could use Script: Add PDF highlight annotations from Kindle MyClippings to add your Kindle annotations to the PDF.