After changing the automatic numbering setting for folders in the settings tab, the change has not affected the folders currently in the data room.
Changing the numbering setting in the Settings tab will affect all folders (new and old) except the numbering setting and schema were changed within specific folders, then it wouldn't apply to those folders.
To change the numbering settings on your current folders:
Go to the Documents tab
Right-click on the directory (top-level folder) you'd like to change and choose Edit Details
Change the numbering setting and schema to your liking or click the tiny hyperlink "Reset to Deal Default", then click Save.