The midfielder is now set to join Championship rivals Swansea City.
Bowyer told the club's official website: “I'm disappointed. I didn't see this coming if I'm honest, which makes it harder to take. At the end of the day, though, we have to move on.
“He's been a credit and a pleasure to work with. He's come in and put his body on the line every single day. He's scored us goals and helped us win games.
“For someone so young, he's a great talent to work with, and I wish him all the best for his future."