In the Advanced Field Mapping dialog, one can specify to Use remaining estimate if present as the third option of Task Duration Calculation Mode.
This is a good feature and very useful if you want to support an ongoing planning process, where you always wanna focus on the issues' currently estimated effort when it comes to scheduling.
However, this task duration calculation fails if the Remaining Estimate of an issue has been decreased to 0 (which basically signals that the task is done). In this case, the plugins update mechanism obviously falls back to the Original Estimate field, which is extremly confusing because in this scenario, the original value carries a totally outdated estimation result.
Therefore, I guess the plugin should differentiate between a state where the Remaining Estimate field has never been set during an issues lifecycle and a state where the Remaining Estimate just has decreased to zero simply because the issue is done.
The fist variant requires the "fallback" on the Original Estimate (as it is currently implemented), however, the latter should update the regarding MS Project field with 0.