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Not all values are saved, yet. The configuration file saves coordinate reference information. In essence, the information that the exporter needs in order to extract proper info from SW each time.
I believe limit mates are respected in the latest version of the exporter. If you want to create an easy export, add limit mates to each joint that represent the limits of the joint itself. I think the soft limits are set to the same thing as the hard limits in the urdf. Create an configuration solely for export with these limit mates unsuppressed if you don't want to deal with them in the future.
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