Just a thought to stop the first chord in a new song coming up as C just set the key sig of the song to the chord you want.
However if you want to start on a note in a key that is not the tonic that is a problem.
But you can always change the first chord yourself anyway.

Starting a new version of song for part 2 to stitch on as a wav, I guess you would need to end part one on a key signature bar before it reaches its critical bar number for you.
At a point that makes musical sense of the arrangement currently generated.
Then create part 2 set to that key sig. the problem then being you may have to regenerate multiple times to come up with same arrangement that the software came up with in part one.
You may well struggle here a bit as what was say bar 220 of a song in part one
In your part two song will be back at bar one and may well get treated as an opening phrase, and therefore not sit well, with where the arrangement would have gone in a continuous generation of more bars.
You will also have to negate the count in at some point .

Seems a rather messy workaround to me and a bit hit and miss

Just my take

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