I fixed the problem I was having.
I changed the MPEG4ENC.manageOutBufs line in the server combo config to
[false, false...] instead of [true, true...].
I am not entirely sure what this does, but my guess is that some cached
memory was preventing a proper delete of the algorithm instance.
It works now.
I still think a command that completely restarts the encoder without
deleting it and restarting would be nice.