Google Photos can backup any folder that contain photos
as long as you select them. The Camera folder gets backed up by default, but you have to toggle on backup for any other folders, since many folders can contain app-related images that most users would not want to backup (like stock images, cached ad images, etc.).
At this point, it's starting to look like the update process glitched. This can unfortunately happen from time to time. This is only speculation, but it could be due to a poorly coded update, which would not be entirely surprising given LG's notoriously poor record for system updates.
Have you already used a file manager app to look through every possible directory that's accessible to the user? Make sure the file manager is set to show hidden files/folders as well.
Recovering deleted files on internal storage would require rooting, so that may be more trouble than it's worth, but you can read this guide:
[Guide] Recovering Deleted Files - Android Forums at AndroidCentral.com. Since those files weren't technically deleted by you, maybe an app like DiskDigger or Recuva still be useful even without rooting.