Thomas underwent surgery on the ankle on Tuesday morning after the club decided resting him for two weeks would not guarantee a full recovery.
Football manager Geoff Walsh said that given the 12 to 16 week recovery period, the club was hopeful that Thomas's rehabilitation program would have him back by about round 20.
Although Thomas was undergoing surgery on the same ankle that kept him out for the first three rounds of the year, the injury came as a result of a kick Thomas received during the game against Hawthorn in round three.
Dayne Beams will not return until at least after the bye with the club taking a conservative approach to his rehabilitation from a quad injury.
Walsh said Beams had not had a setback, but scans showed that last year's best and fairest winner was not yet ready to step up his training.
"There was a danger of setting him back to square one so we have taken a real conservative approach there, pulled him back for an extra couple of weeks. Let's see how things are after the bye," Walsh said.
Walsh admitted Beams was frustrated and the club was a bit surprised when scans showed his progress was a bit slower that expected.
"For Dayne to have not played a game to date - best and fairest winner, had a great break out year last year - it's super-frustrating," Walsh said.
Thomas comes out of contract at the end of the season and had indicated earlier in the year he wanted to delay negotiations until he had recovered from his initial ankle surgery.
When asked whether the time out would enable Collingwood and Thomas to start intense contract negotiations now, Walsh's response was to the point.
"I would not have thought the two are connected, no," Walsh said.
