Aspects of a multi-protocol storage device including a controller are provided which handle mode switches after a shutdown resulting in a large amount of unfinished work by phasing the work during and after initialization. The controller operates in a first mode such as an SD mode and a second mode such as a NVMe mode. In the event of a shutdown in the second mode resulting in unfinished work, the controller initializes in the first mode. During initialization, the controller determines whether a completion time for the unfinished work exceeds an initialization time in the first mode. When the completion time exceeds the initialization time, the controller performs a first portion of the work during initialization and postpones performance of at least a second portion of the unfinished work until after initialization. As a result, initialization timeouts in the first mode due to the unfinished work may be avoided.