Topic: having game data on System Memory and USB at the same time

I have an externally powered hard drive that at some point I started using with my Wii U. I have noticed on rare occasions it is not recognized when the Wii U boots up. I think this is the main thing that has caused me to have save data on both USB and System Memory. I would notice if my save game was gone but I have kids playing the console as well . By default most of my save data was on system memory for disc based games except I put Breath of the Wild on USB. I had the USB issue once and thought my game got erased but realized there wasn't a new game update and the only reason the game installed an update was because my USB wasn't being recognized. I was able to conclude the new save data on system memory is the one I had to delete. The proper thing to do was erase the data off system memory so my USB data could be used again. Worked fine.

I noticed I have other games that have data in both places. I don't understand why as these are disc based games. Doesn't data on system memory always take priority over USB? That is what I saw when I had Breath of the Wild in both spots. So why would these disc based games be saving to USB ever? Because System Memory was full when the game was first launched? I don't recall my system memory ever being full. Did I choose to download an update to a disc game to USB for some games by happenstance? ( I only recall doing this for breath of the wild but I guess i am not the only one who uses the console)

It seems impossible to tell for sure on these other games which save data is being used. Isn't it always going to save data to system memory first? If so why would it ever save to USB? I was able to deduce why Breath of the Wild was on both and which I wanted to keep, but did these disc based games originally get chosen to download updates to USB as well? I am not sure.

My USB drive usually works and since I think System Memory takes priority is it safe to assume that when these games are usually played they are running off System Memory? If this is the case it should be safe to move the system memory game data to overwrite USB so that the usually used save is now the only save. I should probably then move all the disc games to system Memory so I don't have issues caused by USB not being recognized and creating double data.

The alternative is to check for duplicate data, load the game with USB connected and boot the game to see if it's the right save, then disconnect USB and boot the game again and see if it's the right save, determine which data to keep. That seems very tedious. Please tell me the first idea is sound.