The first question that needs to be addressed is whether you can have two people read the megillah to be yotzei.The Rivevos Ephraim 7:209 was asked this question. The Magen Avraham 692:2 writes that if the one who is reading the megillah loses his voice then the second person taking over has to start from the beginning. From this Magen Avraham it seems certain that one should not do this lechatchilah ,rather if someone loses their voice then one should take over,but must start from the beginning.
However, Shu"t Aseh Lecha Rav 4:42 writes that one is yotzei bedieved in such a case,and if it is not a bother for the tzibbur the second reader should start from the beginning.The Elya Zuta 692:4 writes that in such a case the second person starts reading from the place the first person stopped,and one doesnt make a new bracha. He compares this to shofar where one does not need to repeat the blasts nor a new bracha. This does not compare to Torah reading which is connected to the brachos which are connected to the individual. This is not like megillah which the bracha is made for the tzibbur. He also notes that the ending bracha is not connected to the megilla per se and therefore a second person can continue the reading from the place the first one left off.
Now to your question,the switching of megillos shouldn't really make a difference since they are both kosher megillos and the mitzvah is to read from a kosher megillah. Also the halacha of not returning the wrong sefer Torah because of the honor of the sefer Torah(Kaf Hachaim 144:13) ,who says this applies to a megillah which is of much lesser kedusha? Tircha d'tziburah is a factor even by a sefer Torah taken out accidentally and in some cases may be returned in order not to inconvenience the tzibuur(Igros Moshe OC 2:37). Regarding brachos ,I think the Elya Zutah can be applied in this case. Regarding hefsek the Shulchan Aruch 690:5 writes even if one paused long enough to finish all of the text still he has fulfilled his obligation. The Rema writes even if he speaks he is yotzei. Tircha D'tziburah is subjective ,since some people may not mind and other might. You have to know your congregation.
It should be noted that the Shulchan Aruch 690:3 writes : צריך לקרותה כולה ומתוך הכתב ואם קראה על פה לא יצא וצריך שתהא כתובה כולה לפניו לכתחלה אבל בדיעבד דאם השמיט הסופר באמצעה תיבות אפי' עד חציה וקראם הקורא על פה יצא
One can technicality read up to half the words of the megilla(depends what parts of the megilla,some are integral and cannot be missing) by heart and be yotzei bedieved.