Flores could miss Swansea's date with Bradford after suffering an ankle injury in the emphatic 4-1 win over QPR.
Swans boss Michael Laudrup admits an injury to one of his key players is an unwelcome headache, just two weeks before the Welsh club's first major cup final.
He said: "We have to wait to see if it is only a twisted ankle or it could be more damage with the ligaments.
"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."