[Quoth]

Arrgh!
The bug regarding chapter and % progress of the location of annotation is back. Annotations seem to have chapter & progress last used at last sleep or power cycle?

"Annotations" in Digital Editions in the Root is still a file (the previous method to fix the bug).
Also the epub is on the SD card (Original H2O).
I did have this bug with previous firmware, but either of these two tips from davidfor cured it.

I'm trying again with a fresh copy of the book, (deleted it) and with "Update Metadata" now unticked... Except when I reconnect and restarted, the "Update Metadata" was ticked again!

Edit:
Unticked it and restarted Calibre AGAIN and the tick comes back.

Edit 2:
I'll try the epub on main memory as the Annotations folder doesn't exist, the firmware update didn't delete my empty file. Which is still an empty text file according to the Linux text editor.