A data processing system comprises a pool of reconfigurable data flow resources with arrays of physical configurable units, a controller, and a runtime processor. The controller is configured to generate a hot-plug event in response to detecting a removal of an unallocated array of physical configurable units from the pool of reconfigurable data flow resources. The runtime processor is configured to execute user applications on a subset of the arrays of physical configurable units and to receive the hot-plug event from the controller. The runtime processor is further configured to make the removed unallocated array of physical configurable units unavailable for subsequent allocations of subsequent virtual data flow resources and subsequent executions of subsequent user applications, while the subset of the arrays of physical configurable units continues the execution of the user applications.