Do you know which format you'd like the merged org to be: PTO or PTA?
In general, it shouldn't be a problem. You may not want to formally merge as much as shut down one and become the other as a whole. You could even change the name of the remaining org (name change isn't very hard) to be more broad.
I am the PTA Treasurer of a middle school serving 7th and 8th graders. We have a separate school and PTO that serves only 6th grade. In the next couple years the schools will be merging and I'm looking for advice on merging the two organizations. I am particularly concerned about any laws regarding the merging of our assets, since one organization is a PTO and the other is a PTA.