Batch processes are susceptible to long term production failures that adjacent intermediate storage cannot absorb totally and therefore force the shut-down of adjacent units. Because batch processes have many timing constraints, a careless storage operation leads to the propagation of the failures along the production line which results in a great additional loss of productivity. This article develops operational algorithms for the basic MIMO storage system in the presence of failures of the processing units, up or down-stream of the storage facility. Specially, we consider a class of long term failures which affect all or a subset of the multiple input/output streams. Algorithms are carefully designed to satisfy physical constraints and fully utilize the storage capacity, while minimizing the duration of forced shut-downs. An example study simulating failures demonstrates the effectiveness of our approach.