You have to migrate SQL database (MySQL, SQLite) best way is make SQL dump. There are three databases for ccnet, seahub and seafile.
Run what you want I have experience with Win servers, and everytime is there some problem ... Security, stability. Have alot Linux servers without problems, restarting after update. Best thing is Windows update which force restart without warning and only solution is kill Windows update service. 2 win servers hacked by system bug. Only one Linux server hacked by low root password(customers IT guy is idiot). One Linux server have 4 years run time with actual kernel and security updates. Everytime I'm saying ... Use what you want but don't want on me to use it and don't come with problems to me.