In "Manage Storage", check individual content from internal or external media isn't working.

Hey there TinFour.

If the DLC isn't being registered at all, the issue may come down to your current storage option. Are you using an external or internal storage device? If you're saving externally, try moving that content to internal storage to see if there's a change. Alternatively,
try downloading the content onto a different external device.

Even if you add an external HDD the internal one will still be usable, but If my memory serves me right you can set it so that the Xbox one installs New games to the external drive instead of the internal one

You can manage the games/content on Your HDD's in "My games & apps"... Select a game and press the menu button on Your Controller, the Select manage game then you will be able to move or copy content between Your drives/storage Devices..

support.xbox.com/.../manage-storage

I'm attempting to move all storage from internal to external, but when I go to manage storage and select the external there is no option to set as default, only view & format. Any suggestions?

I'm using a Seagate Backup Plus 2TB 3.0 usb external hdd and I haven't had any problem at all. Below is a copy and pasted article for info on external hdd and FAQ.

A 256GB or larger storage device with USB 3.0.

Note: Any brand/drive should work, as long as it's at least 256GB and USB 3.0.

Note: You can connect up to two storage devices at the same time

Note: If the storage device is connected via a USB hub, it needs to support USB 3.0.

Note: Both USB powered and AC adapter powered will work.

External Storage FAQ

Q: What can I install on my external storage device?

A: You can install games, downloadable content, and apps on your storage device.

Q: Can I store game saves on the external storage device?

A: No. Game saves are automatically stored in the cloud and synced to the Xbox One console.

Q: Can I use the external storage device for music and video playback?

A: No. For the initial release of the external storage feature, media files, including music and videos, are not supported. We are considering this for a future release.

Q: Can I copy or move a game from my internal hard drive to my external storage device?

A: Yes. Check out the content management features by going the Manage page for the game or app.

Q: Can I use my external storage device with my PC as well as my Xbox One?

A: No. The external storage device will be formatted for use by the Xbox One console only. PCs won’t recognize the drive partition created by the Xbox One.

Q: Can I re-format my storage device from my Xbox One console?

A: If you'd like to remove all content from your storage device and start over, you can re-format your storage device on the Xbox One. To do this, go to Settings>System>Manage Storage, choose the external drive you want to format, and select Format. After
this is done, the Xbox One will treat it as a brand new drive.

Note: Formatting causes the storage device to wipe all data.

Q: Do I need to bring my game disc while roaming with my storage device?

A: Yes. The external storage device does not change the licensing for games, so if the game was installed from a disc, the disc is required to play the game.

Do you know if the missing games are on internal or external storage? It sounds like the Xbox is not seeing the external drive. Try unplugging your external storage and doing a full shutdown of the Xbox. While it is off, plug in the external drive and then
turn the Xbox back on. Go to Settings > System > Storage and see if the drive is there. From there you can also view the content of both internal and external drives.

Hope this helps