In our experience, it is an advantage being dealt with by one of these specialist units. The inspectors in the units have a better understanding of R&D, so it is easier to explain why your activities are research and development. One of the problems we had prior to the setting up of these units, was having to deal with inspectors who had no understanding or experience in this area. 

In our experience, the transfer does not increase the risk of an enquiry. HMRC have a well-established sampling and risk management system to select cases for enquiries and claiming R&D Tax Credits should not have any effect on this.