I have a vehicle that has many sub assemblies, for this conversation were talking suspension. What are the restrictions using a designed or simplified assembly to create the mates? I've yet to track down the exact issue, but say i have the simplified asm. hiding many component and now i need to see them, I'll switch to designed assembly and go about my work, then I'll try to reposition the suspension and all (or many) mates are broke. I'll go back and forth activating, and switching to simplified again to regain the mates.
I just now had this issue and couldn't get them to remate, luckily i didn't save the assembly, so I closed it, reopened and was able to switch to designed and move the suspension.
Should assembly mates work regardless of the configuration?
What version of SE are you running? The relationships with assemblies that have simplified versions should maintain. And you can't place a relationship on a simplified version of a part or assembly, so you should be good there. Is the part you placed the relationship to still contained in the sub-assembly?