diff --git a/CHANGELOG.md b/CHANGELOG.md
index 77f9808435..2f3f200306 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ All notable changes to this project will be documented in this file.
 - [GUI] Protect upgradeable mods from being displayed as uninstalled (#3944 by: HebaruSan)
 - [GUI] Restore conflict highlights in changeset (#3948 by: HebaruSan)
 - [GUI] Conflict highlight for selected row (#3951 by: HebaruSan)
+- [Core] Fix uninstallation of manually deleted files and directories (#3955 by: HebaruSan)
 
 ## v1.34.0 (Minkowski)
 
diff --git a/Core/ModuleInstaller.cs b/Core/ModuleInstaller.cs
index ad68893080..21add3212c 100644
--- a/Core/ModuleInstaller.cs
+++ b/Core/ModuleInstaller.cs
@@ -771,6 +771,14 @@ private void Uninstall(string identifier, ref HashSet<string> possibleConfigOnly
                             file_transaction.Delete(absPath);
                         }
                     }
+                    catch (FileNotFoundException exc)
+                    {
+                        log.Debug("Ignoring missing file while deleting", exc);
+                    }
+                    catch (DirectoryNotFoundException exc)
+                    {
+                        log.Debug("Ignoring missing directory while deleting", exc);
+                    }
                     catch (IOException)
                     {
                         // "The specified file is in use."