They couldn't start with a clean sheet - that's the whole point behind the structure of the deal. If Flybe went bankrupt - which appears to have been imminent given the £2.2 million purchase price and the immediate £20 million cash injection - then the Heathrow slots would have reverted to BA as insolvency would have been a default under the slot lease agreement. To keep the Heathrow slots, Flybe had to stay in business and so the low purchase price behind the deal recognises that the new owners of the business will - if the transaction goes through - have to take on a lot of liabilities which they would have been able to wash away in a CVA or an administration. The cash from the Gatwick slot sale will probably tide them over for a week or two until negotiations with the card providers can take place to unblock some of the forward ticket sales and the £20m "loan" - aka emergency cash injection - goes in. Once / if the deal is complete, then the £80m injection is the clean-up money needed to sort out the mess and recapitalise the business.
Sad to see a company so systematically destroyed by mis-management in such a short space of time.