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Sometimes when you make changes to a filter tool or some other tool's configuration and immediately click on another tool on your workflow, the chanegs you made to your first tool won't register. The only way to get them to register is if you click the canvas afterwards.
Sounds like this may be a bug. We will try to reproduce on our end to see if there is a systemic problem with hw configuration is saved. On a similar note, we have been talking about the option of reflecting changes to configuration even before you click on another tool or the canvas. One place where this would be nice is when there is an error. It'd be nice if the error went away without having to leave the tool or click the "apply" button.