A fantastic read below on the Honda RA109 which was separate to the BGP001, some very cool stuff could be have been on the Brawn, possibly making it dominate as much as Merc are this season
http://www.racecar-engineering.com/articles/f1/hondas-secret-f1-car-revealed/
During Honda’s whole ’3rd era’ F1 project it had multiple R&D teams working on car design. In reality there were three main Honda development teams, the main one being at the Honda F1 team in Brackley, England, but in addition to that there was Honda R&D in Tochigi, Japan and finally the smaller HRD facility in Bracknell, England which was primarily concerned with the engines.
When Honda decided to withdraw from F1, the R&D department at Brackley stopped work, when it restarted it was focussed on creating the Brawn BGP001, but the R&D team in Tochigi had continued with the RA109 for much longer than anyone realised.
http://www.racecar-engineering.com/articles/f1/hondas-secret-f1-car-revealed/