Yes you can make changes to it by adding, replacing and/or deleting files or even entire folders and then recompile it all back into a BIN file to re-flash to region 48 using xrgn. It was intentional that i didn't mention that possibility in my previous post because of the very real risk of bricking if somehow the process isn't perfect. Even if you make the new BIN too big the flash may fail badly. Because you already cannot access preboot there is no way to fix anything if it also cannot use SD card. It's highly likely you would lose that function because a bricked device likely won't enter far enough into the boot process to read the SD if it's been bricked by corrupt files onboard. If the data connection problem's caused by a PCB component failure then re-flowing won't fix it.
Safest way is to use ergn command to remove from the internal memory any map, poi or other files which can easily be used on the card. That way if there's a problem you can just remove the card and the device will still boot. Most brickings are actually due to corrupt IMG and GPI files. You're better to not copy new poi's to the device from the card when prompted because of that reason. Some files such as Voice need to remain on the devices itself of course but updating them isn't crucial.
You really should try to reflow the USB socket solder connections and reinforce its attachment points to the board. If you can re-enable the PC data connection all this goes away. Better to find out now for a couple of reasons if reflowing will work.