There are too many changes with evolution for this to be canon with literally NO explanations... So I feel I should drop a few theories.
1. The Towers.
The Towers on Evolution were the towers used all alone, and the towers in the original Code Lyoko (the visual we saw) was an outer shell for what is now the Evolution Towers. The outershell to which was lost in data corruption.
2. The New Supercomputer.
Sometime between Echoes and XANA 2.0, the factory was discovered by a business owner, who simply, by luck, made it to the supercomputer. He deemed it old and unsatisfying, and decided to put all the sofeware onto a newer CPU. When having wasted money on it, when it has a bunch of locks and codes, and stuff he couldn't dream to understand, he goes back to and sticks to the upper floors, eventually giving up on the factory for it being too rundown, and him being in too much of a whole.
3. The New Sewers
Because of a rat problem, the got some cement, and paved the insode, and to make SURE no rats could escape, the raised the manhole, and made it more complicated to get in. There boards and scooters...well...got lost in the clutter of their rooms or something
4. Samantha Suarez
Unfortunatley, and I know this is gonna piss alot of people off...SAMANTHA SUAREZ AND SAMANTHA KNIGHT ARE TWO ENTIRLEY DIFFERENT PEOPLE. Odd's attachment to the new Sam, well, lemme explain. Something happened to Samantha Knight (death possibly), and Odd chased after the next best. Someone with the same name and back story. Her attitude towards him stems from well, the fact that she knew him for more or less a year.
5. Odd's hair
Bad haircut
6. Ulrich's Random Height change
Puberty's a b*tch
7. Changes in their rooms.
Someone decided to decorate. Duh.
Anything else left unexplained, leave in the comment section below.