Parent it in batches; such as parenting 100 parts at a time then waiting a second, use greedy meshing if possible to reduce the part count (i know some players might not want this, so maybe a setting the player can toggle?), or parent the minimum amount of things you can parent and have the clients create the rest of the instances, like the client creates welds, motors, etc based on tags or names or what the parts are parented to.
@fastkingyaya, runtime unions created on the server are slow and clunky, would not recommend
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