Your booking reference and flight reference are two different things.

Your booking reference is sent via email after your booking has been confirmed. Please make sure you have checked your spam or junk folder. Sometimes it can take up to 72 hours for you to receive the confirmation email, so don't worry. You will need this reference for logging on to 'My Account' and when your speaking to us.

Your flight reference is needed for anything flight related. You'll need this to check-in or add on any inflight extras. 

Your flight reference can be found on your invoice/confirmation. Your flight reference is in the flights section of your Thomas Cook invoice and labelled Airline reference, an example is shown below.

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Airlines can sometimes refer to this as a PNR if you need to talk to them at all.