Before your foot get shot

Will your (previous) annotations apply if you swap for KEPUB??? Probably not.
Someone who HAS replaced an EPUB with annotations, with A KEPUB will need to answer this.
Next The order you DO DO this needs LOTS OF care (assumes they survive).
Do not remove the EPUB until the SECOND connect or you will orphan the annotations.
(The first disconnect makes the DB entry on the Kobo. the second is where the additional metadata happens. In this case, you hope to use the original DB entry when you add a version.) You will need to verify EVERY BOOK shares the same data. There is so much that can glitch that
I would leave the existing stuff alone.