The entire reason the if statement exists is to only flush and print when done if flag is true
This avoids /save-all from hurting as much as it was before, such as from backup plugins.
This was not applied correctly, and would completely blow up chunk entity
registration if this feature was turned off....
Additionally, change how the entities are removed to be more consistent with other code.
Surface some of the logs indicating there is a problem as we are having so many issues with
entities that we don't need to be surpressing logs like that.