I think bits of the detail are missing but starting from the beginning.
1) Has the seller returned the £5,000
2) You say the lease of the cafe has been assigned/transferred to your son, if this is correct then a licence to assign would have been entered into, three people would have to agreed to this a) The seller b) The buyer c) The Landlord.
3) To undo this, the same 3 people would have been involved.
4) Now if I were the seller I would not allow the lease of my business to be transferred until I had all the money in my bank.
5) If you are correct and the seller has transferred the lease to your son, then his only option is not to sell your son the fixtures and fittings, but equally the seller has no premises to trade from.
I suggest you get the full story from your son.