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This sounds like you are making it too complicated. Your handle can be an arbitrary integer that gets incremented by 1 all the time. You have a hash table mapping these to entity pointers. Entities store their handle on themselves. The end.
Stuff like "generational index" is an implementation detail that you don't want to serialize because when you read that back, it won't match your system's current values! (I don't do things this way, but if you did, yeah, it's an internal detail).
