As @JonathanM said, they ARE the same file. If you look at the share, it will contain files from the cache drive and from the share itself. If you delete the file from the user share and that file happens to still be on the cache drive, then you're deleting the file from the cache drive because it is 100% the same file as what's appearing on the user share. It's not a duplicate, hardlink etc. It's the same thing
All shares are nothing but a combination of all the files stored within say /mnt/disk1/media, /mnt/disk2/media, and /mnt/cache/media. This combined view is the exported share of /media, or if you're looking at things via the command prompt, /mnt/user/media.
Your problem with the media management share is most likely the split level. To be quite honest, this concept also messes me right up but I don't particularly care about it as I couldn't give 2 cents as to where the file(s) wind up. It doesn't bother me if S01E01 and S01E02 are on different disks. Look at https://wiki.unraid.net/UnRAID_6/Shares