What did the terms and conditions say?
If the holiday is actually provided by Thomas Cook then their conditions state that they can change your flight times by up to +/- 12 hours without compensation.
https://www.thomascook.com/ota/pdf/Booking_Conditions_and_Holiday_Information.pdf
If it's provided by another operator but just booked through Thomas Cook then it might be different.
Personally I think this 12-hour rule should be challenged under the unfair consumer contracts legislation. It's obvious that a holiday with flights in the middle of the night is completely different to a holiday with flights in the middle of the day, and you'd expect it to be significantly cheaper, so the idea that they could switch you from one to the other without compensation is palpably unfair.
The Office Of Fair Trading, as was, looked into package holiday contracts in 2004 and published guidance on what they considered to be unfair terms.
https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/284435/oft668.pdf
Your rights when the operator makes changes before departure are addressed on page 13 and following.
The Thomas Cook booking conditions are narrowly compliant with this, as you'd expect. They allow flight times to be changed by up to 12 hours. So on the face of it this doesn't give you much comfort. However there a couple of angles which I think are worth pursuing.
- The OFT guidance points out (page 15) that exhaustive lists of "significant" changes are vulnerable to be deemed as unfair, because "some alterations, though not generally considered fundamental by some consumers, may be important to others". And Thomas Cook do not claim that their list of "significant" changes is exhaustive: they say that the changes which they consider significant include change of airport, change of destination, change of timing by more than 12 hours, etc. So I think that gives you scope to argue that the timing changes are very significant to you, taking into account the special nature of the holiday etc.
- The OFT recommend (page 17) that "terms providing for compensation, even if they have a scale as a yardstick, should allow for payments that reflect the actual loss of the consumer". Thomas Cook's terms provide for the tabulated compensation amounts to be increased "in appropriate circumstances".
So I think that's your approach. Write to them, and politely point out the OFT guidance that the definition of "significant" change and the amount of compensation payable can be flexible. Explain the special nature of your holiday and the inconvenience and additional cost which this would impose on you, and ask them to do the decent thing.
Good luck!
Disclosure: I am not a lawyer. However last month I successfully obtained £1500 compensation from a double glazing firm after a botched installation, by following this exact approach. They initially denied liability until I politely pointed out that the relevant OFT guidance suggested otherwise. No need to make any threats or anything: they quickly came round to my way of seeing the issue!
EDIT: The regulations governing the industry are the Package Travel, Package Holidays and Package
Tours Regulations 1992.
http://www.legislation.gov.uk/uksi/1992/3288/contents/made
These do
not enshrine the 12-hour timing change rule. They simply require that "significant alterations to essential terms" must be notified to customers ASAP and must allow customers to cancel without penalty. So there is clearly scope for Thomas Cook to interpret "significant" in a more flexible way.