Consider a matrix job with an axis "axisOne" and and an axis "axisTwo", and a combination filter of axisOne.endsWith("bar").
Now use the job-dsl-plugin to update that job so that it now has an axis "axisThree" and no combination filter at all.

The result is a half-updated job with the original (unmodified) combination filter, and an exception (and failed job-ds-plugin build step) saying:

groovy.lang.MissingPropertyException: No such property: axisOne for class: groovy.lang.Binding
at groovy.lang.Binding.getVariable(Binding.java:63)
at org.jenkinsci.plugins.scriptsecurity.sandbox.groovy.SandboxInterceptor.onGetProperty(SandboxInterceptor.java:224)
at org.kohsuke.groovy.sandbox.impl.Checker$4.call(Checker.java:241)
at org.kohsuke.groovy.sandbox.impl.Checker.checkedGetProperty(Checker.java:238)
at org.kohsuke.groovy.sandbox.impl.Checker$checkedGetProperty.callStatic(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:194)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:230)
at Script1.run(Script1.groovy:1)
at org.jenkinsci.plugins.scriptsecurity.sandbox.groovy.GroovySandbox.run(GroovySandbox.java:141)
at hudson.matrix.FilterScript.evaluate(FilterScript.java:45)
at hudson.matrix.FilterScript.apply(FilterScript.java:85)
at hudson.matrix.Combination.evalGroovyExpression(Combination.java:101)
at hudson.matrix.Combination.evalGroovyExpression(Combination.java:91)
at hudson.matrix.MatrixProject.rebuildConfigurations(MatrixProject.java:646)
at hudson.matrix.MatrixProject.onLoad(MatrixProject.java:509)
at hudson.model.AbstractItem$1.call(AbstractItem.java:674)
at hudson.model.AbstractItem$1.call(AbstractItem.java:672)
at hudson.model.Items.whileUpdatingByXml(Items.java:135)
at hudson.model.AbstractItem.updateByXml(AbstractItem.java:672)
at javaposse.jobdsl.plugin.JenkinsJobManagement.updateExistingItem(JenkinsJobManagement.java:497)
at javaposse.jobdsl.plugin.JenkinsJobManagement.createOrUpdateConfig(JenkinsJobManagement.java:149)
at javaposse.jobdsl.dsl.JobManagement$createOrUpdateConfig$5.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at javaposse.jobdsl.dsl.JobManagement$createOrUpdateConfig$5.call(Unknown Source)
at javaposse.jobdsl.plugin.InterruptibleJobManagement.createOrUpdateConfig(InterruptibleJobManagement.groovy:37)
at javaposse.jobdsl.dsl.JobManagement$createOrUpdateConfig$5.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at javaposse.jobdsl.dsl.JobManagement$createOrUpdateConfig$5.call(Unknown Source)
at javaposse.jobdsl.dsl.DslScriptLoader$_extractGeneratedJobs_closure4.doCall(DslScriptLoader.groovy:183)
at sun.reflect.GeneratedMethodAccessor20003.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:56)
at java.lang.reflect.Method.invoke(Method.java:620)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2056)
at org.codehaus.groovy.runtime.dgm$162.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at javaposse.jobdsl.dsl.DslScriptLoader.extractGeneratedJobs(DslScriptLoader.groovy:176)
at javaposse.jobdsl.dsl.DslScriptLoader.this$2$extractGeneratedJobs(DslScriptLoader.groovy)
at sun.reflect.GeneratedMethodAccessor21493.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:56)
at java.lang.reflect.Method.invoke(Method.java:620)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:384)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
at javaposse.jobdsl.dsl.DslScriptLoader$_runScripts_closure1.doCall(DslScriptLoader.groovy:61)
at sun.reflect.GeneratedMethodAccessor21276.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:56)
at java.lang.reflect.Method.invoke(Method.java:620)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2068)
at org.codehaus.groovy.runtime.dgm$164.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at javaposse.jobdsl.dsl.DslScriptLoader.runScripts(DslScriptLoader.groovy:42)
at javaposse.jobdsl.plugin.ExecuteDslScripts.perform(ExecuteDslScripts.java:316)
at hudson.tasks.BuildStepCompatibilityLayer.perform(BuildStepCompatibilityLayer.java:78)
at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:779)
at hudson.model.Build$BuildExecution.build(Build.java:206)
at hudson.model.Build$BuildExecution.doRun(Build.java:163)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
at hudson.model.Run.execute(Run.java:1728)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:405)

What should happen instead is that the MatrixProject's validation code should be deferred until after the job-dsl-plugin has finished updating the job (which would have removed the combination filter).
i.e. validation should be done on the final product, not on a mixture of the old and new job.

(also, personally, I think that an invalid combination filter should merely be a warning - users can manually enter invalid filters so we should allow this via the job-dsl-plugin too)

The workaround was to manually go in to the problem job (which took some effort to find as that DSL build step defined dozens of jobs) and remove the combination filter, "save" the new job and then re-run the Jenkins job that contained the DSL build step, at which point everything went green again.