Save data, dlcs and other extra data for games needs to be on the same device the game is stored on. So if you were to install your disc based games to a usb device, you would also have to copy save data and dlcs from the Wii U's internal storage to the usb device. I explained how it worked earlier in the thread, since you need to follow the steps in a certain order to get it to work, so let me just quote my post from back then:
How to copy save data and dlcs from disc based games to the USB device:
1. First of all, the game can't be installed to the USB HDD / flashdrive before moving or copying save data and dlc from the Wii U's system memory to USB. If it is installed already, you'd have to delete the game through the Wii U's data management and install it again using WUPInstaller after moving the savegame / dlc to USB.
2. To copy the savegame and the dlc if available, head into the Wii U settings and from there into the data management options
3. You should see an option to copy, move or delete data. Choose that and then head into the system memory.
4. Press X on the gamepad to enter data moving mode but do not be confused - this mode allows you not only to move but also to simply copy savegames, dlc and any other extra data for games to USB.
5. After pressing X, choose the games you wish to copy the data from and then press Y. Confirm your choice by hitting the copy button and savegames, dlc and other extra data from the games chosen before will be copied to the USB device.
6. At this point install the game to USB using WUPInstaller. Upon starting the game from USB next time, the savegame you used with the disc version before will be there and ready as well as any dlc you bought for the game.