The Spaniard was stretchered off 30 minutes into the easy victory after twisting his ankle in making a clearing header, and he was spotted leaving the Liberty Stadium on crutches.
A fracture has been ruled out and Flores will travel to Dubai for next week's warm-weather training camp, but boss Michael Laudrup admitted he was concerned over the defender just two weeks before their big date at Wembley.
"We have to wait to see if it is only a twisted ankle or it could be more damage with the ligaments," Laudrup said.
"We have to wait for the scan but if it is ligaments he would definitely be out of the final.
"We will see first if there is anything that needs surgery, the more things we can exclude right now the better.
"If it is ligament damage we need to see how bad it is and make a decision from there."