Consider following setup:

1. the repo on GitHub has 2 branches
2. I clone the repo and now can see these 2 branches ("one" and "two") under "REMOTES > origin" in sidebar of SourceTree
3. then on GitHub somebody removed branch "one" and adds branch "three"
4. after doing fetch from "origin" remote the branch list is: "one", "two", "three" and not "two", "three"

This is because branches that are removed on remotes (if that removal was done outside of SourceTree) are not removed in SourceTree as well.

To fix this currently I need to do:

1. rename "origin" to "origin2"
2. rename "origin2" to "origin"