I was playing the game just now from external with this new fix. First I noticed some longer loading times, but I was playing from internal before so I didn't think much of it. Then it froze in the very first chapter in the bar, in that bathroom scene. Then I restarted it using select+x for bd-emulation. Now it had much longer loading times. Also when a cutscene started it just went to black, I had to press start to pause and then select continue before it loaded.
Then in the part where you play as young nate, in that evening scene where you go back to the museum, it stopped loading textures all of a sudden, and i was walking on empty air which should have been rooftops.
So I quit the game, started up multiman so copy it back to internal to see if it helps, and it's suddenly removed from the games list. Now I hooked up my external HDD to my PC, and discover that all the game files are gone, only the update folder remains.
So I'm putting it straight back on my internal hdd, and launch it from there to see if the problems are gone, but I'm guessing there are still some bugs with this fix.