Error thrown when field layout scheme is pointing to a non-existent project

A user reported the following error when importing. Even though it has been fixed this is just for reference.

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When upgrading for 3.1 to 3.4.1, when Jira is upgrading my data (after import) I get this error:

java.lang.RuntimeException: JIRA appears to contain a fieldlayoutschemeassociation record referring to a nonexistent project.
at com.atlassian.jira.upgrade.tasks.UpgradeTask_Build82.createFieldLayoutScheme(UpgradeTask_Build82.java:138) at com.atlassian.jira.upgrade.tasks.UpgradeTask_Build82.doUpgrade(UpgradeTask_Build82.java:124)
at com.atlassian.jira.upgrade.UpgradeManagerImpl.doUpgradeTaskSucess(UpgradeManagerImpl.java:671)
at com.atlassian.jira.upgrade.UpgradeManagerImpl.runUpgradeTasks(UpgradeManagerImpl.java:567)
at com.atlassian.jira.upgrade.UpgradeManagerImpl.doUpgrade(UpgradeManagerImpl.java:393)
at com.atlassian.jira.upgrade.UpgradeManagerImpl.doUpgradeIfNeeded(UpgradeManagerImpl.java:341)
at com.atlassian.jira.upgrade.UpgradeManagerImpl.doUpgradeIfNeededAndAllowed(UpgradeManagerImpl.java:301)
at com.atlassian.jira.upgrade.UpgradeLauncher.contextInitialized(UpgradeLauncher.java:65)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3692)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:4127)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:759)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:739)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:524)
at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:603)
at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:535)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:470)
at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1118)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:310)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1020)
at org.apache.catalina.core.StandardHost.start(StandardHost.java:718)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1012)
at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:442)
at org.apache.catalina.core.StandardService.start(StandardService.java:450)
at org.apache.catalina.core.StandardServer.start(StandardServer.java:680)
at org.apache.catalina.startup.Catalina.start(Catalina.java:536)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:275)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:413)

Looking at the database, there are indeed four rows that are orphans. Deleting the rows fixed the problem.