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I don't like it but maybe it's the right option for you. Just don't expect Studio One to second-guess what you intend exactly by saving under a different name. All these non-standard save options require some degree of user awareness of what it does and where goes what exactly. You ran into a problem of Studio One looking in a different place than where the intended file was. The problem looks like being related to having same-name files in different places. For me that's a warning light to be extra careful with file management, moving songs, etc. Otherwise you may run into problems like you had with your song.