A line current differential protection system that uses an external time reference continues providing protection to a power apparatus upon the loss of the external time reference. An external time reference synchronization mode and a channel based synchronization mode may be selectively applied on a per channel basis such that only those channels in the system that are not guaranteed to stay symmetrical use external time reference synchronization. When the external time reference is lost, fallback strategies may be used such as disabling or de-sensitizing the line current differential protection function, switching from the external time reference synchronization mode to a channel based synchronization mode with appropriately selected protection settings, and/or marking the channel as unavailable to isolate the system from the consequences of synchronization errors over this channel and instead using a master-slave mode with other available channels to continue providing line protection with the current differential system.