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Mstern,
Since you ask the question in the context of O&M, are you reverse engineering the system to establish allocated baselines?
I'm trying to clarify what you are asking because -- ideally establishment of the Allocated Baseline(s) would have begun back in the system life cycle process where the system requirements were being defined and the system design was being created (and probably be "finished" by the time the O&M stage was begun).
If in fact you are reverse engineering the allocated baseline(s), then my answer to your question would be "as soon as you can."
Since the system is already established, probably the first step would be to identify the components of the system. The probably next step would be to record (document) the current functional, performance, interoperability, and interface capabilities of or within the system (and assume that those currently accurate). Then you can parse (allocate) those requirements to each component. Reverse engineering assumes that the current operation of the system and components are in accord with what was required at the beginning. Basically, this is sort of a "cart before the horse" approach.
Under a more "classic" approach, a project would use the allocated baseline(s) to dictate what the various components are supposed to do, and then the system and components would be built to those specifications. Either this wasn't done or I'm totally not understanding the question.