You can do it by duplicating the "first" residue after itself using mutate_insert and merge_atoms. Then mutate_replace the first residue to whatever residue it is going to be, and sam_rename to correct the residue names:

        Lys2-Gly3-Glu4---
              |
            Mut_insert   (makes empty entry)
            Merge _atoms (duplicate coords)
              |
              v
        Lys2-Lys2a-Gly3-Glu4---
              |
           Mutate_replace
              |
              v
        Ala2-Lys2a-Gly3-Glu4---
              |
           Sam_rename, Move_zone
          (Ala1 will initially be on top of Lys2)
              |
              v
         Ala1-Lys2-Gly3-Glu4---

Perhaps you should do a

 Write_formatted mol_* save_file ;