Have you been able to access the upgraded database in Desktop yet? If no, you can simply run upgrade one more time and choose "Traditional user store". If you need to change to Portal user store, make sure you set the same portal (or ArcGIS online if this is the portal you connected when upgrade in Pro) as active portal in ArcGIS Administrator. That way when you access from Desktop, it will prompt you to log in.
For the Task Assistant issue, if you configured the task in Desktop, the task file cannot be opened in Pro. You will need to reconfigure it. The steps are:
1. Create the task in Pro. The task file you create in Pro has format as *.esritasks. Refer to the following help topic if you have any question on how to create task files in Pro.
Create a new task—ArcGIS Pro | ArcGIS Desktop
2. As the following screenshot shown, export the task file into your workflow manager database.
3. Configure the task in the step of your workflow to be used in Pro.
Hope it help.
Thanks,
Meggie