Opening a file outside MobileSheets is going to import it. You are seeing a file conflict, and when that occurs, MobileSheets is asking how it should handle the fact that there is already a PDF with the same name in the storage location. Overwrite just means overwrite the file, but a new song will still be created. I should mention that this only happens if MobileSheets does not recognize that an existing song already exists that uses that same file in the storage location. In that situation, you'll see a different option appear - "Update Existing Song with New File". That would do what you are expecting. My recommendation is not to import the file from outside MobileSheets, and instead select the song on the library screen, tap the three dots at the top right and then "Swap File". You can then swap in the new version of the PDF.
Mike
Mike