After I checkd better every single particle system I had has broken links now, there is not a single sub emitter that is working… is it supposed to be like that after the update? 
No this sounds bad. What version are you upgrading from?
Are all subemitter links being lost during upgrading? Does it happen from a fresh project in the old version with a basic subemitter setup?
Can you submit an example project made in the old version as a bug? Please post the case number back here when you have it. We can then look into this as a matter of urgency.
Thanks!