I have imported and exported e-mail messages in Windows Live Mail several times over the years. I recently had to do that again to recover from a bad install of Windows 10.  When I import messages they go into a storage folder called imported messages. All logical...  Now I want to put them in the same folder structure as before.  I drag the folders around in the left panel until the structure looks like I want it. I delete any empty items and then delete everything from the deleted items folder under Storage Folders.  OK, all looks good. However, now I wonder where these items really are on my C-drive. In File Explorer (as it is called now in Windows 10) I have enabled viewing of hidden files, systems files, etc in order to actually see this kind of stuff. I follow the path:

C:usersmyusernameAppDataLocalMicrosoftWindows Live Mail

Now comes the mystery...  The folders are all mixed up in hierarchy.  There are legacy levels of folders and subfolders named Imported Folder. I can find actual messages (with cryptic file names) deep in this unexpected hierarchy. Apparently Windows Live Mail doesn't actually move stuff on the drive, just rearranges pointers. It is not clear if what I thought was deleted is actually deleted or just the pointer removed. I find there are a bunch of legacy folders that were apparently restored from backup.  Windows Live Mail no longer sees any of this because they were likely from previous accounts, etc.

I think it is time to clean up this mess! If I use File Explorer to move this stuff around into a sensible structure, will Windows Live Mail lose track of it? What can I safely delete among the mystery folders that don't contain my current stuff? What invisible system files are really needed within the Windows Live Mail folder? Note, I am using POP3 on this desktop. Any advice on how this actually works and what I can safely clean up would be appreciated.

Also, I have a different issue with contacts.  The Windows Contacts folder has much redundancy with the Windows Live Mail contacts folder, but it is not completely the same. If I export and import I will need to manually clean up a bunch of redundancies. Same problem occurs when I import from a backup.  Is there any way to merge these while automatically eliminating redundancy. What if I just copy from one place to another then import a whole cleaned up Windows Contacts folder after deleting contacts in Windows Live Mail. In any case I don't want to lose contacts.  Any help here would also be greatly appreciated.