I don't think this spells doom at all.
It is not impossible that whilst helping to co-ordinate the exodus, Starbuck and Boomer run into troubles. It has always occured to me that after taking the colonies with a Fleet ff basestars, did the Cylons really let a Battlestar and Fleet of small ships wander out unnoticed ?
There IS room for this storyline here, and it will help flesh out this area of the story. I hope he develops his own adventures whilst sticking to the continuity of the original series.
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