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We have also been considering CAE files in Windchill for some time.
However, as youhave already pointed outthere are issues around file size and the fact that there is no PDMLink integration for most CAE packages.
We have not implemented anything yet regarding native CAE filesbut have considered the following:
If the CAE files are stored withina Document rather then Reference Document it is possible to associate them to a particular iteration of the WTPart.