The 26-year-old "Twilight" star went to ground last week after Stewart sensationally apologised for having a fling with director Rupert Sanders, who she worked with on "Snow White and the Huntsman", reported Us magazine.
Pattinson is currently staying at his "Water for Elephants" co-star's ranch in Ojai, California, the same place where she got married to Jim Toth in March 2011.
"He was a total mess. He's questioning everything. He doesn't know what to do," a source said.
Stewart, meanwhile, was rumoured calling and sending texts to him.
"She's dying to save the relationship," another source said.
There were a lot of rumours surrounding the pair since pictures showing Stewart getting cozy with her "Snow White and the Huntsman" director came out.
One of the latest stories said that the couple was in dispute over the custody of their adopted dog. He allowed her to keep her cat Max but wanted her to leave the pooch to him.