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.