This was always going to happen - there's historic precedence that enquiries receive ALL information and then decide themselves what is relevant and what isn't. It's not like Johnson's "can you get some milk on your way home" messages or anything more private than that are going to get published.
Stuff like this really makes me think that the government should have its own secure messaging service. Make it look and act like WhatsApp if you want, but if you're a government minister or senior civil servant you should get a government phone and are only allowed to communicate with other officials via this service. That way it can be secure, and if content needs to be scraped for an enquiry it's easily done.