Moving Projects with Duplicate Filenames Across Drives?

I just returned from a trip to Japan where I used a Sony RX10mkIII camera to shoot UHD video of my trip. I did the editing on an Asus gaming laptop and took advantage of the fast internet in the Tokyo region to upload each night from my apartment.

Now that I'm back in the States, I tried copying my project files and content to a drive on my main editing workstation and have run into a problem:

On some days of the trip, my day spans two SDXC cards. The problem is that the camera starts the numbering over again from C0001 as soon as it detected a new card. Naturally, when copying these to the laptop, I got a duplicate file warning. So what I did was make a sub folder called "card 2" and put the files from the second card in there to avoid overwriting earlier files from that day. This worked fine on the laptop, but became a problem when I copied everything and tried to relink the footage at home.

What I'm encountering is that I have duplicate entries in my project (ie., two instances of C0001) and both are from the top folder in the drive. Premiere CS6 didn't link the files in the "card 2" folder--it simply placed a second copy of the top folder's C0001 where card 2's C0001 should have been loaded. As a result, many of the timelines have the wrong footage appearing in them.

I tried manually relinking the card 2 footage, but there seems to be no way to do it all at once, and relinking each piece of footage is taking 180-20 seconds for the machine to become responsive again so that I can right-click the next thumbnail and repeat the process. I have perhaps 150 files I need to relink. Is there a faster way to accomplish this in a batch?