UPDATED 8/14/2018:
As we previously announced in MC138148, we will be providing an option to opt out of the versioning setting update. You can start opting out today using SharePoint Online Managem...
Updated Aug 22, 2018
Version 8.0
Blog Post
If you open the SharePoint folder from the Web View, you can click on the ... (three horizontal dots) next to the file in question. A menu will pop-up and one of the options should be "Version History". If you click on Version History, all of the versions will pop-up. There are three vertical dots next to each version along with the modified date. If you click on the three vertical dots, another menu will pop-up with a delete option. You can use this capability to delete all of the versions you no longer need, presumably the older ones from before you added the meta-data.
The deleted files will go to the recycle bin which still consumes storage quota. If you are satisfied with the deletions you can permanently delete them by first deleting them from the SharePoint recycle bin, and then delete them from the Second-stage recycle bin. The link to the Second-stage recycle bin is at the very bottom of the display of the recycle bin. You have to scroll all the way down to see it.
Once you delete the undesired versions from the Second-stage recycle bin, their storage quota should be released.
Warning: Please be aware that I think deletion from the Second-stage recycle bin is permanent, and there will be no way to recover those versions.