diff --git a/spring-boot-project/spring-boot-tools/spring-boot-configuration-processor/src/main/java/org/springframework/boot/configurationprocessor/MetadataCollector.java b/spring-boot-project/spring-boot-tools/spring-boot-configuration-processor/src/main/java/org/springframework/boot/configurationprocessor/MetadataCollector.java
index b9e4f0e3c6..ea06d3091b 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-configuration-processor/src/main/java/org/springframework/boot/configurationprocessor/MetadataCollector.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-configuration-processor/src/main/java/org/springframework/boot/configurationprocessor/MetadataCollector.java
@@ -111,7 +111,7 @@ public class MetadataCollector {
 	}
 
 	private boolean deletedInCurrentBuild(String sourceType) {
-		return this.processingEnvironment.getElementUtils().getTypeElement(sourceType) == null;
+		return this.processingEnvironment.getElementUtils().getTypeElement(sourceType.replace('$', '.')) == null;
 	}
 
 	private boolean processedInCurrentBuild(String sourceType) {
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-configuration-processor/src/test/java/org/springframework/boot/configurationprocessor/IncrementalBuildMetadataGenerationTests.java b/spring-boot-project/spring-boot-tools/spring-boot-configuration-processor/src/test/java/org/springframework/boot/configurationprocessor/IncrementalBuildMetadataGenerationTests.java
index dd7b1b6e78..8e2f91ae33 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-configuration-processor/src/test/java/org/springframework/boot/configurationprocessor/IncrementalBuildMetadataGenerationTests.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-configuration-processor/src/test/java/org/springframework/boot/configurationprocessor/IncrementalBuildMetadataGenerationTests.java
@@ -23,6 +23,7 @@ import org.springframework.boot.configurationprocessor.metadata.Metadata;
 import org.springframework.boot.configurationsample.incremental.BarProperties;
 import org.springframework.boot.configurationsample.incremental.FooProperties;
 import org.springframework.boot.configurationsample.incremental.RenamedBarProperties;
+import org.springframework.boot.configurationsample.simple.ClassWithNestedProperties;
 
 import static org.assertj.core.api.Assertions.assertThat;
 
@@ -92,4 +93,12 @@ class IncrementalBuildMetadataGenerationTests extends AbstractMetadataGeneration
 				.has(Metadata.withProperty("bar.counter").withDefaultValue(0).fromSource(RenamedBarProperties.class));
 	}
 
+	@Test
+	void incrementalBuildDoesNotDeleteItems() throws Exception {
+		TestProject project = new TestProject(this.tempDir, ClassWithNestedProperties.class, FooProperties.class);
+		ConfigurationMetadata initialMetadata = project.fullBuild();
+		ConfigurationMetadata updatedMetadata = project.incrementalBuild(FooProperties.class);
+		assertThat(initialMetadata.getItems()).isEqualTo(updatedMetadata.getItems());
+	}
+
 }