The downloading of the feats should not alter the character, it only adds content and does not remove or alter anything.
Are you able to add the feats again to the character? If you exported your character it is possible to do a rollback by importing it again, otherwise I am afraid that a rollback is not possible. Your characters and other added content do not get synchronized with a server.
I also have this problem i seem to be missing improved and greater two weapon fighting as well as other PHB1 feats.