Pending new lease registrations

I am assisting some leaseholders with their acquisition of the freehold. They are almost ready to proceed and sign the transfer however it has come to light that there are a couple of new leases pending against the freehold title which belong to two of the leaseholders who are purchasing the freehold. I am wary of proceeding to complete the transfer of the freehold until these new lease applications have been completed as, if there is any issue with the new leases and the applications are cancelled for any reason and the freehold gets transferred then I am not sure whether new applications could be submitted against the freehold given that the freehold will have changed hands and the "landlord" named on the lease will no longer be the landlord named on the freehold. However perhaps my thought process is incorrect? I would be very grateful for any advice on this.

Laura - there's not too much advice we can offer here as it's really legal and not registration advice you need.
One of the key aspects to any conveyancing is ensuring that the order of events is understood and before you complete on any transaction that you understand what is already registered, waiting to be registered and how each then impacts on your own transaction.
If I have read your post correctly you have a freehold purchase to complete so you have a freehold tenure but two 'new' leases yet to be registered. A conveyancer would be checking the legal ownership and what the 'new' leases involved and what their impact would be on the freehold - ultimately both would be registered against the freehold, presumably mirroring those already present.
If, in your worse case scenario, the two new leases were to be cancelled and not registered, and you had already and completed on the freehold purchase and applied for that to be registered, then the freehold purchase application would take priority over any resubmitted new leases. Quite possible and in my experience what would then happen is we would seek the consent of the new freeholder to registration of the new leases, as they had not originally granted them.
The 'priority order' of such applications to register is a keystone of conveyancing and registration. It is one of the basic reasons that lengthy wait times between submission and actual registration rarely pose an issue for owners as they are protected by that 'priority order'. So if that priority order changes in the way you are thinking then there's still a way forward providing of course everyone is in agreement - and it would be odd for the new freeholder to say NO re the two new leases I suspect as they are already aware of their existence and the legal position as a result.
That's a very simplistic way of looking at what can be a complex scenario legally but may offer some help.

That's really helpful, thank you very much.