A method, system and computer program for controlling operation of an automated storage and retrieval system (1) during rebuilding its physical design. The method comprises a planning and designing phase where a new design is established and were storage columns (105) with a rail system (108) that is affected by the rebuilding are excludes from a selection of available routes for container handling vehicles (201) operating on the storage system (1), a relocation phase where storage containers (201) located in excluded storage columns (105) are relocated to other storage columns (105), a rerouting phase were traffic flow of container handling vehicles (201) are rerouted according to available routes and where the master controller (220) is instructed to control the vehicles (201) according to the available routes, a rebuilding phase were the storage system (1) is rebuilt according to the new physical design, and a final routing phase were the routing planner (200) controls traffic flow of the vehicles (201) according to available routes on the rail system (108) of the rebuilt physical design.