As of Scaffold DIA 4.0.0, on Linux and Mac operating systems, if you search mzML files, the workflow parameter, SKIP-MSCONVERT=true, will be set and Scaffold DIA will not run MSConvert. On Windows, MSConvert will always run, except in the case where you manually set SKIP-MSCONVERT=true in the workflow.
The workflow file will need to be edited in order to force this operation. A quick and easy way to do this is set up your experiment, then export the workflow file, find it on your filesystem, and edit it in a text editor. Save the file and reload it in the Load Data dialog in Scaffold DIA.