A lot of software has the ability to open files from an earlier version, for backward compatibility, if you want to then use it in the new software it is advisable to save as a different file. If newer software mangles old files without prompting, then that is not a good thing - it should either prompt to ask if you want to continue if it needs to changes saved data, or at least give the oportunity to save in the old file format with lost functionality... I can't comment on what compatability exists between ds3 and ds4, but suspect that there is very little commonality in the file versions?

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