If there is no audio file to read Onenote treats the file as if there never was a file to begin with. You won't see the audio icon in that note until the audio file is restored.
Let me check that before you go deleting things...
While removing the audio does not doing anything to the note reintroducing the audio does not resync. Once the audio is removed it appears that you are out of luck. Let me try moving the audio instead of deleting and restoring it.
The note will still realize it has a recording attached to it, but it won't sync. If you bring up the audio toolbar you can play it back, but it won't highlight the notes nor will you get nice speaker icons next to your notes. What format are you recording in? The default quality for recording can record an hour in under 5 megabytes, surely that's small enough for you to handle. Unless you record an hour or two a day, I suppose.