After 6 weeks, you can contact the Czech CAA.
I'm not sure if 6 weeks is something that comes from the EC regulation, implementation guidelines, or Czech law, but the CAA is pretty clear in that you should file a complaint with them if you haven't heard back in 6 weeks after submitting the claim.
FWIW: I had a flight delay due to mechanical that caused me to lose a connection. I submitted a claim through form, after 4 weeks sent a reminder to an email I found online (saying I will be forced to forward to CAA and consider other lawful steps), in another week they confirmed my claim.