It just looks like an administrative tidying up exercise to me.
I think there is much more to it than that. Apologies if I do not get this 100% right and start some "fake news", but here's how I believe it to be.
To complete the full shift of Old Flybe assets and slots into New Flybe, there had to be a period where both companies held their licences. This had to last beyond 3 June as that's the date on which winter slot allocations are given out by slot coordinators. The CAA / Shapps decision to revoke Old Flybe's licences means that this parallel running now can't happen and so the winter slots of Old Flybe have lapsed and can't be obtained then moved across to New Flybe. The CAA is almost at pains in its announcement to differentiate between New Flybe (Flybe Limited) and Old Flybe (FBE Realisations 2021).
The timing of the announcement on 3 June may be a coincidence but it certainly does not look like one.
New Flybe has an Operating Licence and could start commercial flights tomorrow if it wanted to. What's changed on the back of the CAA decision is that it now hasn't got the winter season slots of Old Flybe - it would have to go get its own slots.
New Flybe is just as able to start flying as it was before. But it has lost the benefit of Old Flybe's slots, and so I guess if this was a really a "slot play" as has been suggested, we'll now see for sure. Slots aren't exactly hard to come by at most regional airports if it is genuinely serious about starting as a UK regional airline, so time will soon tell.