Timeline sound recording would be a useful tool to have in Keynote, however Recorded Slideshow is limited by replacing the sound recording from a specific slide onwards, the original recording is removed from the start of the new recording onwards.
I never use recorded slide show for this reason, I use QuickTime and GarageBand to record and edit then place the sound files either on each slide or as a continuous in Soundtrack.
If you want to preserve the existing recording try this, its a reasonable one off workaround:
- 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
- Save
- go to Inspector > Document > Audio and drag the exported sound file from the desktop on to the Soundtrack well
- save