diff --git a/xwiki-commons-core/xwiki-commons-extension/xwiki-commons-extension-api/src/main/java/org/xwiki/extension/job/internal/AbstractInstallPlanJob.java b/xwiki-commons-core/xwiki-commons-extension/xwiki-commons-extension-api/src/main/java/org/xwiki/extension/job/internal/AbstractInstallPlanJob.java
index 392b276044..f50a773623 100644
--- a/xwiki-commons-core/xwiki-commons-extension/xwiki-commons-extension-api/src/main/java/org/xwiki/extension/job/internal/AbstractInstallPlanJob.java
+++ b/xwiki-commons-core/xwiki-commons-extension/xwiki-commons-extension-api/src/main/java/org/xwiki/extension/job/internal/AbstractInstallPlanJob.java
@@ -1301,7 +1301,17 @@ private Set<InstalledExtension> getReplacedInstalledExtensions(Extension newExte
         throws IncompatibleVersionConstraintException, ResolveException, InstallException
     {
         if (getRequest().isInstalledIgnored()) {
-            return Set.of();
+            // Even when installed extensions are ignored for the plan, we still need to include the currently
+            // installed version (if any) as a "previous" extension so that the install job can properly replace it
+            // using the UPGRADE flow (which correctly unregisters then re-registers the extension in the installed
+            // extension repository, instead of failing with "already installed").
+            Set<InstalledExtension> previousExtensions = new LinkedHashSet<>();
+            InstalledExtension installedExtension =
+                this.installedExtensionRepository.getInstalledExtension(newExtension.getId().getId(), namespace);
+            if (installedExtension != null && installedExtension.isInstalled(namespace)) {
+                previousExtensions.add(installedExtension);
+            }
+            return previousExtensions;
         }
 
         // If a namespace extension already exist on root, fail the install
diff --git a/xwiki-commons-core/xwiki-commons-extension/xwiki-commons-extension-api/src/main/java/org/xwiki/extension/repository/internal/local/LocalExtensionStorage.java b/xwiki-commons-core/xwiki-commons-extension/xwiki-commons-extension-api/src/main/java/org/xwiki/extension/repository/internal/local/LocalExtensionStorage.java
index 3e27bd7a6a..4e180fa04b 100644
--- a/xwiki-commons-core/xwiki-commons-extension/xwiki-commons-extension-api/src/main/java/org/xwiki/extension/repository/internal/local/LocalExtensionStorage.java
+++ b/xwiki-commons-core/xwiki-commons-extension/xwiki-commons-extension-api/src/main/java/org/xwiki/extension/repository/internal/local/LocalExtensionStorage.java
@@ -310,7 +310,7 @@ public void removeExtension(DefaultLocalExtension extension) throws IOException
         // Delete the extension descriptor file
         try {
             Files.delete(extensionDescriptorFilePath);
-        } catch (FileNotFoundException e) {
+        } catch (IOException e) {
             LOGGER.warn(
                 "Couldn't delete the extension descriptor file [{}] when removing extension [{}], "
                     + "because it doesn't exist. Root error: [{}]",
@@ -323,7 +323,7 @@ public void removeExtension(DefaultLocalExtension extension) throws IOException
             // Delete the extension file
             try {
                 Files.delete(extensionFile.getFile().toPath());
-            } catch (FileNotFoundException e) {
+            } catch (IOException e) {
                 LOGGER.warn("Extension file [{}] was not found while removing [{}] extension",
                     extensionFile.getAbsolutePath(), extension.getId().getId());
             }
@@ -333,13 +333,13 @@ public void removeExtension(DefaultLocalExtension extension) throws IOException
         Path extensionVersionFolderPath = extensionDescriptorFilePath.getParent();
         try {
             // Delete the extension version folder
-            Files.delete(extensionDescriptorFilePath);
+            Files.delete(extensionVersionFolderPath);
 
             // Try to delete the extension folder
             deleteExtensionFolderIfEmpty(extensionVersionFolderPath.getParent());
         } catch (DirectoryNotEmptyException e) {
             LOGGER.warn("Extension version folder [{}] was not empty after removing the extension [{}]. Keeping it.",
-                extensionDescriptorFilePath, extension.getId().getId());
+                extensionVersionFolderPath, extension.getId().getId());
         }
     }