Don't just assume that it will happen - I know of (and have heard about) Trusts who've had a PFI build but excluded the EBME / Medical Physics department from the deal because they wanted to keep the service in-house.
If you have a good relationship with the senior clinical people, particularly the consultants, start raising the issue with them and try and get them on your side. If they see the change as "losing" your department, they'll support your case for staying in the Trust.
