You can do it a couple different ways, the plugin can only create index files of your content and won’t ever modify/delete any of your content (unless I guess you had some existing files with the same names as the auto-generated index files?)
If you have some higher level folder that contained all your 10-19, 20-29, etc. folders, you only need to enter the higher level folder name in the ‘Folders included’ section.
Alternatively, if you leave the ‘Folders included’ section blank, it will generate index files for every folder in your vault, including the base vault folder.
Another way is have the plugin generally index everything in your Obsidian vault, except for the folders you specify in the ‘Folders excluded’ setting.