SWBKCB
I think you're right.
Yesterday all the SEN Stobart Air/Flybe routes were bookable on the Virgin website under VS flight numbers - as they have been for a couple of weeks at least. All that was needed was to fly the next few days flights under the normal STK flight numbers for flight planning etc. and to notify booked passengers that their flight number will change to VSxxxx. Additionally issue a press release advising that future passengers should book via the Virgin website, listing all the routes that they were 'rescuing' for the already booked pax.
I think that may well have been the plan in case Government funding was not forthcoming but along came the worsening Covid-19 situation in recent days so "Naaah, let's not go there."