Provided are a system, memory controller, and method for using counters and a table to protect data in a storage device. Upon initiating operations to modify a file in the storage device, a storage write counter is incremented in response to initiating the operations to modify the file. In response to incrementing the storage write counter, write table operations are initiated including setting a table write counter to a storage write counter and setting a table commit counter to the storage commit counter plus a value. The operation to modify the file in response to completing the write table operations. The system commit counter is incremented by the value in response to completing the operation to modify the file.