Sullivan is contracted to the Dragons through 2025 but Flanagan says his management has asked for permission to negotiate with other clubs.
The 21-year-old sought a release late in 2022 only to withdraw the request after talking with then coach Anthony Griffin.
He was linked with Canterbury when requesting a release, however the Bulldogs have since signed Toby Sexton to cover their halves depth.
Both Canberra and Wests Tigers are in the market for a playmaker in 2024.
Flanagan, who will take up the helm in Wollongong in 2024, says he is confident skipper Hunt will remain a Dragon and Sullivan's situation is something the club will monitor.
"With the Ben Hunt situation, he'll be there next year and I've spoken to Ben and I think we've sort of put that to bed," he told the Continous Call Team on Saturday.
"If Jayden goes, he's got the opportunity to look around - he could still be at the club - I think he's a good young player. But if he's got an opportunity somewhere else, we'll consider it later on.
"It's not saying he will or he won't be there. But these things happen all the time at clubs and he's a good young player and I haven't decided either way which way we're going to go there."
Flanagan also confirmed Moses Mbye will depart the club for the English Super League and the Dragons have an interest in signing Hame Sele from South Sydney.
His recruitment drive has been in full swing since he was announced as coach for 2024, meeting with some 15-20 players.
"I've got to be really smart with my recruitment about on and off the field. We're going to make sure that they're going to improve the place off the field as much as they do on the field," he said.
"I'm not going to rush. Shane Flanagan of 10 years ago would have rushed into it and gone and spent all his money pretty quickly. I'll need to be really smart in the way we move over the next six months."
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