First, know your community. My community likes to read things in number order. That makes the MTH renumbering a big deal. Otherwise you could have two books on the shelf with the same title and different numbers.
Second, loop in your cataloging department. Is there a staff member on board who can change the bibliographic records to reflect the new series information? This would be located in the 490 field or could be located in the 245 field under a subfield n.
Third, how are you going to separate your Magic Tree House books from your Merlin Missions books? They both look similar and are by the same author. Only the newly printed titles will have the new series and numbering information on them. For our library, we chose to keep the Magic Tree House books shelved under JFIC OSBORNE and added to the cutter for the Merlin Missions (JFIC OSBORNE/MERLIN). This will help your shelvers to be able to separate out the two series.