After I upgrade to branch API plugin 2.0.4 I start getting these exceptions and all my multi-branch jobs disappear:
java.lang.NoSuchMethodError: jenkins.branch.MultiBranchProject.getRootDirFor(Lhudson/model/Job;)Ljava/io/File;
at com.github.mjdetullio.jenkins.plugins.multibranch.TemplateDrivenMultiBranchProject.getRootDirFor(TemplateDrivenMultiBranchProject.java:306)
at com.github.mjdetullio.jenkins.plugins.multibranch.TemplateDrivenMultiBranchProject.getRootDirFor(TemplateDrivenMultiBranchProject.java:89)
at hudson.model.AbstractItem.getRootDir(AbstractItem.java:177)
at jenkins.model.Jenkins.expandVariablesForDirectory(Jenkins.java:2396)
at jenkins.model.Jenkins.getBuildDirFor(Jenkins.java:2392)
at hudson.model.Job.getBuildDir(Job.java:854)
at hudson.model.Job.onLoad(Job.java:201)
at hudson.model.AbstractProject.onLoad(AbstractProject.java:321)
at hudson.model.Project.onLoad(Project.java:98)
at com.cloudbees.hudson.plugins.folder.AbstractFolder.loadChildren(AbstractFolder.java:597)
at com.cloudbees.hudson.plugins.folder.AbstractFolder.onLoad(AbstractFolder.java:702)
at com.cloudbees.hudson.plugins.folder.computed.ComputedFolder.onLoad(ComputedFolder.java:171)
at jenkins.branch.MultiBranchProject.onLoad(MultiBranchProject.java:175)
at com.github.mjdetullio.jenkins.plugins.multibranch.TemplateDrivenMultiBranchProject.onLoad(TemplateDrivenMultiBranchProject.java:125)
at com.cloudbees.hudson.plugins.folder.AbstractFolder.loadChildren(AbstractFolder.java:597)
at com.cloudbees.hudson.plugins.folder.AbstractFolder.onLoad(AbstractFolder.java:702)
at com.cloudbees.hudson.plugins.folder.Folder.onLoad(Folder.java:107)
at hudson.model.Items.load(Items.java:335)
at jenkins.model.Jenkins$17.run(Jenkins.java:3047)
at org.jvnet.hudson.reactor.TaskGraphBuilder$TaskImpl.run(TaskGraphBuilder.java:169)
at org.jvnet.hudson.reactor.Reactor.runTask(Reactor.java:282)
at jenkins.model.Jenkins$7.runTask(Jenkins.java:1085)
at org.jvnet.hudson.reactor.Reactor$2.run(Reactor.java:210)
at org.jvnet.hudson.reactor.Reactor$Node.run(Reactor.java:117)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

Looks like the bug was introduced in this commit: https://github.com/jenkinsci/branch-api-plugin/commit/4b47cd42505eacfc85dab4f6d3969866ebef25c8