Ok, here are some random ideas:

- ent_purge won't help you AFAIK as it only releases video memory.
- randomizing entities - you usually do this to make cloned entities less noticeable - can also be done with a shader.
- I'd ask JCL about the semantics of ent_morph. If ent_morph does not remove clone data from memory this can maybe be implemented in a future version.
- If you only have few entities to manag you could also create invisible and passable dummy entities for your managment code and let these dummy entites carry their visible counterparts around. This way you could remove the "coulisse" entities and recreate them.