If you have built your enterprise structure in company B you will simply need to delimit the information on your organization units and positions (if you have any Cost Center info attached) and then make the new relationships for the cost centers and new infotype 1008's. That is physically how you do it but there are many questions around your new enterprise structure that need to be answered before this task is accomplished.
Here are the steps I would take assuming your enterprise structure had been defined in company B:
1. Delimit all IT 1001 subtype A011's on all org units and positions that contain old cost centers.
2. Delimit all IT 1008's on org units and positions (there is a good chance that no positions will contain company code information) which contain company A information.
3. Create new IT1001 subtype A011's on the org units/positions previously delimited.
4. Create new IT1008's on the org units/positions previously delimited.
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