No, you cannot change the order of boundaries in BlueKenue and there is no need to change their order. The order is dependent on the geometry of the mesh. Node numbering starts from boundary point with minimum x + y coordinate and goes anti-clockwise along the boundary. Once finished, the inner island boundary nodes are numbered in clockwise direction. However, there is a difference in which island nodes to number first between BlueKenue and Fudda (another software to generate boundary condition file). I am not sure the difference though. This difference does not impact the model results as long as your boundary usage agrees with the boundary conditions file (eg your case file and boundary conditions file both know which boundary has order 1, 2, etc).
Once numbering is done, the order of boundaries is determined. As Riadh suggested, the first open boundary has order 1, the second open boundary has order 2, and so on.
Hailiang