A couple of months after the release of the 50th Anniversary commemorative livery model, the original version of the YZR-M1 in blue was quietly withdrawn. Later still, in April 2006, its place as "Realistic Paper Craft No. 7" was taken by a new version in a red-brown livery, also with no fanfare.
The new version is very similar to the other two, but with some changes to the cowlings (in addition to the colour).
One can only speculate about why this change was made. My suspicion is that the blue livery was too closely associated with the team's former sponsor, Gauloises, and Yamaha and/or the new sponsor decided it had to go.