Self answers to my above questions... In my environment, I deleted the saved searches which were conflicting with my SDF deploy, and my deployments started successfully working again. * In the IDE, opening an SDF suitescript javascript file, editing, and then pressing "Control-U" to upload, will push the file into the wrong location in the file cabinet. However, running a "Deploy" from the SDF project appears to push the script into the correct location in the file cabinet.