Don't think they will replace with Vande Metro. VM will be 12/16 coach while the Agra intercity is running with 20 passenger coaches and can't handle the load of travellers. If even replaced it will not replace Gomti express as distance is 500km and less number of coaches.
Gwalior doesn't have morning intercity to Delhi while opp direction Taj express runs. Vande Metro should run from Gwalior to Nizamuddin I addition to intercity from Agra.