How can I apply my settings from an existing processing method to samples with new or different components?

For research use only. Not for use in diagnostic procedures.

Answer

The option to choose a new reference sample is given, when you either open the method and select a new reference sample on the workflow page, or when you start the results table generation with samples from the new application, browse to and select the old *.qmethod and then use the <edit> option to modify the method.

Within this second workflow the software will choose a reference sample from the data you want to evaluate. 
For both ways you must adjust the components tab (delete selected rows or clear cells) in a second step, until there is no error due to component mismatch left:

When you applied the needed changes for the integration tab the new *.qmethod can be saved and is ready to go.
Like this you can have your setup for the sections Calculated Columns, Flagging Rules and Advanced applied to a new application without the need to import and set everything.