this is exactly what happens if you try and replace the Pictures directory on the new system with the Pictures directory that you have copied to usb. that is because there can’t be two directories of the same name so your system is displacing one with the other.
it might help to think of it like having a car in a one-car garage. you can replace the stuff in the car, but you can’t just drive the new car into the garage and displace the old one.
when i named the album pictures with a small p on my usb, it was to help illustrate the point that i created a new directory instead of copying and pasting the old one as well as to show that copying the contents of a directory is a little more straightforward for what you want to do than trying to copy the entire directory itself 