.s3d is the original zone format that SOE used, newer zones use the .eqg format. Where SOE have updated the zone, they still seem to distribute both the old and the new versions.
The EQ game client looks for the .eqg version first and loads that if present. For some reason, the original version of azone looked for the .s3d file first and generated a .map from that if it found it, or generated a .map from the .eqg if an .s3d version could not be found.
So yes, leave the old version renamed.
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