So, we finally come to the question of rooting, flashing and changing the software. Unless the seller can prove that modifying the software, rooting your device or flashing it with some other OS or firmware was the cause for the defect, you are still covered for defects during those 2 years.
Many manufacturers of consumer devices write into their warranties a paragraph that by changing the software or “rooting” your device, you void the warranty. You have to understand that in EU we have a “statutory warranty”, which is compulsory that the seller must offer by law (Directive 1999/44/CE, §7.1) and a “voluntary warranty” which the seller or manufacturer can, but does not need to, offer as an additional service to the consumer.
In case the seller refuses your right to repair or replace the device, you can sue him in a civil litigation and can report the incident to the national authority.