The midfielder was contracted to play for Ton until the end of the season but had that spell cut short after suffering a fracture which required a wire to be inserted into his arm.
Flannigan, 24, has been informed he faces up to six weeks out before he can return to action but admits his mood was boosted by a visit from the Cappielow gaffer.
Flannigan, top right, said: "The gaffer and Mark McNally came over last week to my house as I was out by then. That was really good of them and I appreciated it.
"I told them that there was no need to come and see me but they did anyway, even though it is a wee bit out of their way.
"That was nice. It was good of them to do that and now I'm just going to have to wait and see when I am able to get back once my elbow has healed."