Can I set the context window BookyAI uses for Ollama models?

Yes, from version 1.9.4. In Settings, under the Ollama model field, choose an "Ollama context window": Automatic (8k tokens, 16k for large models, as before), "Ollama's own setting" (BookyAI sends no context size at all, so whatever you configured in Ollama applies), or a fixed size from 8k to 128k tokens. If you run Ollama with your own context length for other tools, pick "Ollama's own setting": otherwise every switch between BookyAI and those tools forced Ollama to reload the model with a different size.