I might answer too late but I think there is no direct bus. The most siutable train for the bus Sofia-Nis (7.30am) is at 03.01am from Plovdiv and arrives at 05.41 in Sofia. Is that the train you're talking about?
Also there is one bus from Burgas through Plovdiv to Sofia at 4.00am from Plovdiv that goes from North Bus Station (members.virtualtourist.com/m... that I have used 2 years ago. But to be sure you have to contact the company Union Ivkoni (http://www.union-ivkoni.com/offbg-26 - the second result is for North Bus Station) and confirm with them.
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