A system and method for configuring fault tolerance in nonvolatile memory (NVM) are operative to set a first threshold value, declare one or more portions of NVM invalid based on an error criterion, track the number of declared invalid NVM portions, determine if the tracked number exceeds the first threshold value, and if the tracked number exceeds the first threshold value, perform one or more remediation actions, such as issue a warning or prevent backup of volatile memory data in a hybrid memory system. In the event of backup failure, an extent of the backup can still be assessed by determining the amount of erased NVM that has remained erased after the backup, or by comparing a predicted backup end point with an actual endpoint.