Manual connection of atoms

We could very easily have some sort of “re-assign bonding” command.
But what you’re describing is that you want to exclude certain atom
pairs from bonding?

Yes, exclude, maybe with loosing of bonding criteria
I can give an example of incorrect bonding. Attached RES file contains structure of dinuclear complex of iron(II) with trietylenetetramine H2N-CH2-CH2-NH-CH2-CH2-NH-CH2-CH2-NH2. In Avogadro 0.9.6 and earlier versions, it is being read incorrectly, only part of trietylenetetramine ligands present in two molecules (see screenshot Avogadro_1.png)
Then I open this file in Diamond 2 (screenshots Diamond*), where I choose which atoms to connect, and obtain right structure, result of export to xyz and re-opening in Avogadro is given in Avogadro_2.png (one isolated molecule with removed hydrogens)
Possibly difference in programs’ behaviour lies in different algorithms, but I think manual connection in combination with wider ranges of bond lenghts can improve bonds’ recognition