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When publishing a workflow to Gallery or Scheduler (Designer + Desktop Automation) or when packaging a workflow for export, checking the boxes for what to include and what to exclude seems to work inconsistently as of Designer 2020.2. Here is a workaround to cover you until the issue is resolved in a future release.
Versions 2020.2 +
Assets such as macros, files, chained apps, Gallery Data Connections
If you are running version 2019.3.2 - 2019.4.6, then you need to upgrade or refer to this article instead. In versions 2020.2, 2020.3, and 2020.4 (and maybe in some later versions as well) asset management is inconsistent when an asset is used in more than one location within a workflow.
If a file is not packaged with a workflow, then the file will be read from or written to the specified path. (It's important to use UNC path descriptions for unpackaged files if the workflow will be run from a Gallery or scheduled.) If you need more information about asset management, please refer to the links in Additional Resources.
The workaround is to select the Group assets by tool box before you select which assets you wish to package and which you don't. There will probably be more check boxes in this view, so be sure to scroll through the entire group, selecting or deselecting as needed.