Yes, it is the same history file - it is the history sub-folder created in your project folder (unless you chose a global repository in 'Preferences').
There is a quirk in the operation of the option. It doesn't touch the files created before you changed the preference - it only changes the files saved after you make the change to the interval to be saved.
You can manually delete the local history files by selecting the Storage Manager tab, click on the project name in the left display box, click on the type of file you want to delete history for in the right display box, right click to bring up the menu, then click on 'Delete History'. All of the history files for that type of document will be deleted. Again, if the history files are very old, you will have to manually delete them.
This function was apparently made intentionally conservative to keep you from inadvertently deleting all backups.