Nobody knows for sure except Jodi, but judging from their lengthy phone conversations at 3 am and 4 am on June 2, lasting almost an hour total, where Travis was the caller (likely returning her calls) and their subsequent conversations lasting several minutes over the next day and a half, I think it's likely he knew she was coming, and agreed to it. Here's a link you may find helpful:
http://www.hlntv.com/slideshow/2013/02/11/jodi-arias-trial-tragic-roadtrip
Travis' roommate Zach Billings told Detective Flores he saw Travis the morning of June 4 and Travis told him he'd only had 45 minutes' sleep. But Zach also thought he remembered seeing Travis that evening, so he may have had his dates mixed up.
Text messages show Travis repeatedly angry and/or frustrated with Jodi, and friends recalled fights long before that, but we know from Travis' own text messages that he kept taking her back. While he texted her the day she returned to Yreka (April 5 and 6) to stay out of his life, two weeks later he was sending her sweet texts saying "I am at a night club right now and it helped me to come to the conclusion that you are one of the prettiest girls on the planet" and another asking her to send him a naughty picture. In their recorded phone call of May 10, Travis tells Jodi he is coming to visit her in Yreka before he leaves for Cancun, that "You are at the top of the list."
So much for his previous texts to stay out of his life. I see no reason why he wouldn't have welcomed her voluntarily, notwithstanding his angry 5/26 texts. After all, a week after those texts he calls her twice and they talk almost an hour! And continue to talk on the phone for the next day and a half. She slashed his tires twice around Christmas 2007, he told friends she was stalking him, yet he went on vacation with her in March 2008. Despite telling her on April 6 to stay out of his life, his subsequent texts and steamy recorded phone call show he voluntarily remained engaged with her.
Jodi claims he was up watching videos on his computer when she entered the house (he didn't lock the doors) and watched him for a while before he noticed she was there. Since both Jodi and Travis were night owls, it is not unreasonable to believe she arrived around 4 am as she says, and that Travis told her he'd wait up for her. That part of her story sounds believable to me, especially since he'd called her at 3 am and 4 am on June 2 and talked for almost an hour then. Regardless of what time she arrived or how she got into the house, we know Travis and Jodi took nude photos of one another beginning at 1:40 pm on June 4.
btw Travis had only 25 mL, or 1.69 tablespoons of undigested food in his stomach when he died, according to the autopsy report. While Jodi is an inveterate liar, even the best liars weave bits and pieces of truth in their stories, and I think it's possible all he had to eat that day was a bowl of oatmeal, as she testified.