I would like to make subfolders to group pictures/videos by event as well.
Is there a way I can do this locally, and have the remote archive organization updated as well, without retransfering all of the files?
However you mentioned you're using Backblaze S3. I assume you mean you're using their S3-compatible B2 service, and you didn't really say if the software you're using to sync local to B2 is the backblaze software or something else, so it makes it a little difficult to help you.
If the object synced to B2 are keyed in a way that resembles folders, then like S3, to restructure you have to copy the file with a new name with the new folder structure you want.
You can avoid having to do this without retransferring from your machine by using API calls against B2.