The behaviour when Saving ROS packages depends on the input URDF and SRDF files. Cell Editor will never overwrite files that have been processed by the xacro preprocessor, these will instead be saved alongside the original file. Otherwise, the behaviour is to overwrite the URDF and SRDF file that have been opened.
It is possible to open a URDF file without a corresponding SRDF file. In this instance, a .srdf file will be created with the same filename as the URDF file, and placed in the same directory.