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A good way to do it is to keep a staging area of sorts that keeps track of the manually allocated objects and their state. When you allocate you batch all objects to allocate together and then execute the load in one go, updating the records in the staging area. Then, when you're ready to switch to a different scene or whatever, you diff the staging area against the current set of objects that need to be live and deallocate everything else in one go.
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