Flintoff has been sidelined with an injured left ankle since the third Test defeat by Sri Lanka three weeks ago.
"We will have another look in two weeks and see where we are," the 28-year-old told Sky Sports.
"There is scar tissue in there and whether the bone fragments were the result of the operation or were already in there, we don't know."
It is the same ankle where a bone spur was removed in January 2005.
"We are going down the route of physio and exercises to strengthen the ligaments around the ankle," Flintoff said.
"I am not running at the moment, I am doing a lot of cycling. I am doing things that don't cause pain and trying to tick over.
"So far it has been good, there are no adverse affects."
England, who drew the Test series 1-1 with Sri Lanka, went 4-0 down in the five-match series of one-dayers when they lost by 33 runs in Manchester on Wednesday.
The first Test against Pakistan begins on July 13.
