When Tree comes to find Tombs in the first loop of the new universe, his bed is empty not because he's escaped, but because he's been taken down to the OR. We then find out that Lori is the one who did so: which must have been not only how she had the opportunity to set him free in the original universe, it's also how Butler intends to frame Tombs for Lori's murder in the second - he would supposedly have killed her during his hospital escape.
One death scene for Tree has the camera linger around for a couple of seconds to show Carter and Danielle's reactions. Given that the loop always restarts as soon as she dies, Tree wasn't actually dead yet, and (if she was unlucky) still conscious and suffering, even for a short while.
Alternatively, the timelines where Tree dies continue, even after she's dead. There are a dozen timelines where Tree died and didn't come back, including one where Carter just saw her commit suicide in front of him.
