I did add spilt lines to both parts prior to CosmosXpress to created
> resistance and force boundaries. Any suggestions as to what may have caused
> my assembly to go nuts!
When you split a face, SW can lose mates to that face. (I'm not sure if it always loses all mates or if it sometimes manages to save some or all of them. I think it is the latter.) I believe this is because one or both of the split faces now has to have a new name. If you were mated to the part that gets a new name, your mate is broken.
I haven't tried it (I didn't think of it till now), but you might try deleting the split lines. That might, by some mighty miracle, give you a face with the original name and fix the mates.
Jerry Steiger Tripod Data Systems