Avogadro v2 does not have much support for PDB beyond ATOM, HETATM and CONECT records. (Adding support for residues, sequences, etc. is on the need-to-do-soon list.)
So it's known that fields will be removed if you save a PDB file in Avogadro v2.
As to the coordinates.. it sees like you're saying there's a coordinate shift when saving?