That's usually not how these things work. Only parts of the prompt are actually loaded at any given moment. For example, "system prompt" warnings about intellectual property are effectively alerts that the model gets. ...Though I have to ask in case I'm assuming something dumb: what are you referring to when you said "more than 60,000 words"?
The system prompt is always loaded in its entirety IIUC. It's technically possible to modify it during a conversation but that would invalidate the prefill cache for the big model providers.
What you're describing is not how these things usually work. And all I did was a wc on the .md file.