diff --git a/src/index.ts b/src/index.ts
index 4ce81ab..c3b7bb4 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -416,7 +416,21 @@ abstract class Filter extends Plugin {
       return false;
     }
 
-    return (entry || this.input.lstatSync(relativePath)).isDirectory();
+    if (entry !== undefined) {
+      return entry.isDirectory();
+    } else {
+      try {
+        // wrap this in try/catch in case `relativePath` doesn't exist
+        const stat = this.input.lstatSync(relativePath);
+        return stat.isDirectory();
+      } catch (error) {
+        // if we get any other error, we really don't know what is going on so we need to rethrow
+        if (error.code === 'ENOENT') {
+          return false;
+        }
+        throw error;
+      }
+    }
   }
 
   getDestFilePath(relativePath: string, entry: Entry) {
diff --git a/test/filter-test.js b/test/filter-test.js
index 09407bc..0accb83 100644
--- a/test/filter-test.js
+++ b/test/filter-test.js
@@ -96,6 +96,16 @@ describe('Filter', function() {
       expect(filter.canProcessFile('twerp.rs')).to.equal(false);
     });
 
+    it('getDestFilePath handles non-existent (deleted/moved) files', async function () {
+      let inputPath = input.path();
+      let filter = new MyFilter(inputPath);
+
+      output = createBuilder(filter);
+      await output.build();
+
+      expect(filter.getDestFilePath('non/existent/file.js')).to.equal('non/existent/file.js');
+    });
+
     it('getDestFilePath returns null for directories when extensions is null', async function () {
       let inputPath = input.path();
       let filter = new MyFilter(inputPath, { extensions: null });