When using a Spatial ETL tool with an embedded workspace and editing the embedded FMW workspace, the Workbench app launches but the workspace canvas is empty and a Workbench dialog returns a 'file not found' message similar to the following and shown in the image below.
Warning: File 'C\Users\<username>\AppData\Local\Temp\1\ArcGISProTemp45416\sz1k.fmw' does not exist. Would you like to remove it from recent files?
Clicking Yes in this dialog only removes the item on the Recent List of the Workbench app. The FMW file cannot be edited at this point and requires a patch to be editable.
The embedded FMW file is a BLOB field stored with the tool and when tool launches the Workbench app, the creation of the tmp workbench file fails, thus an empty workspace canvas is opened. The embedded workspace itself is still with the ETL tool, you can still open the tool in the Geoprocessing pane and run the tool. You just can’t edit it.
Note: In an instance where the Spatial ETL tool with an embedded FMW file is non-editable, open the .atbx file with 7-Zip to retrieve the embedded FMW file.