Oh, interesting. I want to say there’s a “preserve thinking” option in mainline llama.cpp, but I’m seeing mixed results in my searches and my in-flight internet is not good enough to dig into it properly. Good to hear you have a solution though, because that is likely something I’ll run into as well.
Look for improved templates by "froggeric" on Hugging Face. I use Qwen 3.6 a fair amount using his template and it fixes some issues I saw with the upstream versions.