Since 3.0 I never used 'Apply Context' anymore. I guess they are deprecated but due to older projects they still exist.
Apply context is replaced with better Database/Association/Microflow way to show related data. It filtered the data according to the context but you had no control of the association used for that.
Remove from context was a way to escape from the previously applied context. Should be replaced with a (sub)datagrid with database datasource. For example to show all orders instead of orders of a customer, if customer is the context.
For all places disable the apply context and select the association that is needed to limit the shown data. If an assocation is already selected the only thing you need to do is set 'Apply context' to false.