Keynote is unable to edit a recorded slideshow properly, if you change the slides in any way after creating a recorded slideshow, the slide timings and the slide order become corrupt.
My work around, to preserve the voiceover recording, is to extract the voiceover sound file, make changes to slides, make a new recording for slide timing, then replace the voice over file in Keynote. This takes less than a minute to complete, so its quicker than re-recording.
- with keynote closed, back up the Keynote file (right click >Duplicate)
- open the Keynote file, go to: File > Advanced > Change Filetype and select: Package
- save then close Keynote
- right click the Keynote file then select show package contents, open the Data folder and copy the movie recording file (right click > copy) then paste on to the desktop
- double click the movie file to open in QuickTime player: File > Export sound only then save to desktop
- in Keynote, go to File > Play > Clear Recording
- add, delete or make changes to the slides
- Save
- go to Inspector > Document > Audio and drag the exported sound file from the desktop on to the Soundtrack well
- Save
- make a new "record > slideshow " to add the new timing for slide transitions, the voiceover will not be re-record, so turn the mic volume slider down to zero in: Apple Menu > System preferences > Sound > Input
- do not click on the microphone icon to mute in the recording window
- Save