No one may ever read this topic but I have created my own solution.
1. Remove book from the carousel.
2. Use a file explorer to move the side loaded book from document folder to a temp directory.
3. Remove the additional Kindle created files (mine contained a complete folder with associated files) This is likely where the corrupt file is located.
4. Restart your kindle.
5. Move book back to your documents folder.
6. Open your book and synchronize to furthest page read.
Voila the TtR is working again.
