diff --git a/tycho-core/src/main/java/org/eclipse/tycho/p2tools/copiedfromp2/RecreateRepositoryApplication.java b/tycho-core/src/main/java/org/eclipse/tycho/p2tools/copiedfromp2/RecreateRepositoryApplication.java
index 22573e21f2..017b3f8e13 100644
--- a/tycho-core/src/main/java/org/eclipse/tycho/p2tools/copiedfromp2/RecreateRepositoryApplication.java
+++ b/tycho-core/src/main/java/org/eclipse/tycho/p2tools/copiedfromp2/RecreateRepositoryApplication.java
@@ -151,8 +151,18 @@ private MultiStatus recreateRepository(IProgressMonitor monitor) throws Provisio
                     }
                     Map<String, String> checksumsToProperties = ChecksumUtilities
                             .checksumsToProperties(IArtifactDescriptor.DOWNLOAD_CHECKSUM, checksums);
+                    //remove checksums that are no longer marked for publishing
+                    String checksumProperty = IArtifactDescriptor.DOWNLOAD_CHECKSUM + ".";
+                    for (String property : newDescriptor.getProperties().keySet().toArray(String[]::new)) {
+                        if (property.startsWith(checksumProperty)) {
+                            String id = property.substring(checksumProperty.length());
+                            if (checksumsToProperties.containsKey(id)) {
+                                continue;
+                            }
+                            newDescriptor.setProperty(checksumProperty + id, null);
+                        }
+                    }
                     newDescriptor.addProperties(checksumsToProperties);
-
                     repository.addDescriptor(newDescriptor, null);
                 }
             }