That's a common problem with the Wii U. Like sometimes the games don't launch and sometimes the loader might fail to initialise the drive, so a USB Y cable typically fixes both issues.
My Wii doesn't need a USB Y cable to power the enclosure, so I can't guarantee that a USB Y cable will fix anything for you.
As for why WiiFlow might see the games, that could be due to the timeout period, the cIOS that you're using or how you've formatted the drive.
- Ignore the Wii update
- Restore your NAND backup
- Install cIOS 249 / 250
- Copy your games to your PC
- Clean the HDD with diskpart and format it with Wii Backup Manager
- Move the games back to your USB HDD
- Delete usbloader_gx from sd:/apps and then install a fresh copy
To ensure that the HDD is totally clean and doesn't have any hidden partitions you'd do this.
- Launch command prompt and input "diskpart"
- Input "list disk"
- Input "select disk X" replacing X with the correct drive number
- Input "clean"
- Input "convert mbr"
- Input "create partition primary" and close the popup to format
- Input "format fs=ntfs quick"
- Input "assign"
- Input "exit"
Then from the tools menu in Wii Backup Manager you can format the HDD to FAT32.