The Tecplot format (.plt) overwrites the mesh anyway so is just mesh and data, no boundary conditions: no need to read in the case. Have you tried deleting the non-conformal interface before writing the Tecplot file out?
Depending on what data you need you may find Interpolation files easier to deal with. A colleague has used Python to merge data files before, he used legacy .dat but that was also before the HDF format was available.
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