I would outline the transaction just like you did in this thread and e-mail the information (see information to include below) to CRAHELP@frb.gov. They should be able to give you some guidance.
All respondents that have an institution involved in a merger or acquisition of a branch should send an e-mail to HMDAHELP@frb.gov detailing the merger, the HMDA Respondent IDs, regulatory agencies for the survivor and non-surviving institution(s), and how the filing will be handled (i.e., consolidated submissions or separate reports) for the year of the merger and subsequent years.