diff --git a/org.eclipse.jdt.apt.pluggable.core/META-INF/MANIFEST.MF b/org.eclipse.jdt.apt.pluggable.core/META-INF/MANIFEST.MF
index 697a3c4fec6..188e2459e2b 100644
--- a/org.eclipse.jdt.apt.pluggable.core/META-INF/MANIFEST.MF
+++ b/org.eclipse.jdt.apt.pluggable.core/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %pluginName
 Bundle-SymbolicName: org.eclipse.jdt.apt.pluggable.core;singleton:=true
-Bundle-Version: 1.4.600.qualifier
+Bundle-Version: 1.4.700.qualifier
 Bundle-Activator: org.eclipse.jdt.internal.apt.pluggable.core.Apt6Plugin
 Bundle-Vendor: %providerName
 Require-Bundle: org.eclipse.core.runtime,
diff --git a/org.eclipse.jdt.apt.pluggable.core/src/org/eclipse/jdt/internal/apt/pluggable/core/dispatch/IdeProcessingEnvImpl.java b/org.eclipse.jdt.apt.pluggable.core/src/org/eclipse/jdt/internal/apt/pluggable/core/dispatch/IdeProcessingEnvImpl.java
index bd12734fadc..b14a1dd2305 100644
--- a/org.eclipse.jdt.apt.pluggable.core/src/org/eclipse/jdt/internal/apt/pluggable/core/dispatch/IdeProcessingEnvImpl.java
+++ b/org.eclipse.jdt.apt.pluggable.core/src/org/eclipse/jdt/internal/apt/pluggable/core/dispatch/IdeProcessingEnvImpl.java
@@ -102,7 +102,7 @@ public Map<String, String> getOptions() {
 
 	private Function<Entry<String, String>, String> replacePlaceholdersUsing(Map<String, String> commandLineOptions) {
 		return option -> {
-			String variable, replacement, optionValue = option.getValue();
+			String variable, replacement, optionValue = option.getValue() == null ? "" : option.getValue();
 			Matcher placeholder = Pattern.compile("%([^%]+)%").matcher(optionValue);
 			if (placeholder.find() && (variable = placeholder.group(1)) != null
 					&& (replacement = commandLineOptions.get(variable)) != null) {
diff --git a/org.eclipse.jdt.apt.pluggable.tests/META-INF/MANIFEST.MF b/org.eclipse.jdt.apt.pluggable.tests/META-INF/MANIFEST.MF
index fce02106d04..d2e3ba964bd 100644
--- a/org.eclipse.jdt.apt.pluggable.tests/META-INF/MANIFEST.MF
+++ b/org.eclipse.jdt.apt.pluggable.tests/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %pluginName
 Bundle-SymbolicName: org.eclipse.jdt.apt.pluggable.tests;singleton:=true
-Bundle-Version: 3.6.800.qualifier
+Bundle-Version: 3.6.900.qualifier
 Bundle-Activator: org.eclipse.jdt.apt.pluggable.tests.Apt6TestsPlugin
 Bundle-Localization: plugin
 Require-Bundle: org.junit,
diff --git a/org.eclipse.jdt.apt.pluggable.tests/pom.xml b/org.eclipse.jdt.apt.pluggable.tests/pom.xml
index d19b75809aa..12733a96201 100644
--- a/org.eclipse.jdt.apt.pluggable.tests/pom.xml
+++ b/org.eclipse.jdt.apt.pluggable.tests/pom.xml
@@ -19,7 +19,7 @@
     <relativePath>../tests-pom/</relativePath>
   </parent>
   <artifactId>org.eclipse.jdt.apt.pluggable.tests</artifactId>
-  <version>3.6.800-SNAPSHOT</version>
+  <version>3.6.900-SNAPSHOT</version>
   <packaging>eclipse-test-plugin</packaging>
   <properties>
   	<testSuite>${project.artifactId}</testSuite>
diff --git a/org.eclipse.jdt.apt.pluggable.tests/src/org/eclipse/jdt/apt/pluggable/tests/BuilderTests.java b/org.eclipse.jdt.apt.pluggable.tests/src/org/eclipse/jdt/apt/pluggable/tests/BuilderTests.java
index 57157c1b672..f95830bf54b 100644
--- a/org.eclipse.jdt.apt.pluggable.tests/src/org/eclipse/jdt/apt/pluggable/tests/BuilderTests.java
+++ b/org.eclipse.jdt.apt.pluggable.tests/src/org/eclipse/jdt/apt/pluggable/tests/BuilderTests.java
@@ -415,6 +415,25 @@ public void testBug341298() throws Throwable {
 		fullBuild();
 		assertTrue("Processor should be able to compile with passed options", Bug341298Processor.success());
 	}
+	public void testGHIssue4640() throws Throwable {
+		ProcessorTestStatus.reset();
+		IJavaProject project = createJavaProject(_projectName);
+		IPath root = project.getProject().getFullPath().append("src");
+		env.addClass(root, "test341298", "Annotated",
+				"package test341298;\n" +
+				"@Annotation public class Annotated {}"
+		);
+		env.addClass(root, "test341298", "Annotation",
+				"package test341298;\n" +
+				"public @interface Annotation {}"
+		);
+		AptConfig.addProcessorOption(project, "classpath", "%classpath%");
+		AptConfig.addProcessorOption(project, "sourcepath", "%sourcepath%");
+		AptConfig.addProcessorOption(project, "phase", null);
+		AptConfig.setEnabled(project, true);
+		fullBuild();
+		assertTrue("Processor should be able to compile with passed options", Bug341298Processor.success());
+	}
 
 	public void testBug539663() throws Throwable {
 		if (!canRunJava9()) {