I know you said they're not to appear, and the reason for this is logical, but I think the Wolkenritter could still be mentionned by Nanoha and/or Fate to the Puellae Magi if one of them begins to show signs she's gonna Witch out. Fate talked about her own origins to Homura when she began talking about the Puellae's... depressing situation, but the mention of the Book of Darkness Incident, with the 'nobody left behind' approach, and mention some of their best friends are real persons living millenia ago and who are 'programms' linked to a magical object could lift their spirits.

I'm going epileptic with the second one, but you could also have some speculation about the fact Earth has so few potentials mages because the Incubators are 'culling' potential mages with their action, the "karmic weight" being also the potential power of the Puellae's Linker Cores.

Even if it doesn't perfectly fit for your story, I genuinely think these points are interresting. Hope you think the same way.