diff --git a/config/scripts/file-explorer-deletion-roots-benchmark.mjs b/config/scripts/file-explorer-deletion-roots-benchmark.mjs
new file mode 100644
index 00000000000..d276964861b
--- /dev/null
+++ b/config/scripts/file-explorer-deletion-roots-benchmark.mjs
@@ -0,0 +1,75 @@
+import assert from 'node:assert/strict'
+import { join } from 'node:path'
+import { performance } from 'node:perf_hooks'
+import { fileURLToPath } from 'node:url'
+import { build } from 'esbuild'
+
+const root = fileURLToPath(new URL('../..', import.meta.url))
+const bundled = await build({
+  stdin: {
+    contents: `export { selectDeletionRoots } from './file-explorer-batch-deletion';
+      export { isPathEqualOrDescendant } from './file-explorer-paths';`,
+    resolveDir: join(root, 'src/renderer/src/components/right-sidebar'),
+    loader: 'ts'
+  },
+  alias: { '@': join(root, 'src/renderer/src') },
+  bundle: true,
+  platform: 'node',
+  format: 'esm',
+  write: false,
+  logLevel: 'silent'
+})
+const { selectDeletionRoots, isPathEqualOrDescendant } = await import(
+  `data:text/javascript;base64,${Buffer.from(bundled.outputFiles[0].text).toString('base64')}`
+)
+
+// Original production selector; both paths use the same path-comparison implementation.
+function original(nodes) {
+  return nodes.filter(
+    (n) =>
+      !nodes.some(
+        (other) => other !== n && other.isDirectory && isPathEqualOrDescendant(n.path, other.path)
+      )
+  )
+}
+
+function measure(run, nodes) {
+  for (let index = 0; index < 3; index++) {
+    run(nodes)
+  }
+  const samples = []
+  for (let index = 0; index < 11; index++) {
+    const start = performance.now()
+    run(nodes)
+    samples.push(performance.now() - start)
+  }
+  return samples.sort((a, b) => a - b)[5]
+}
+
+const results = []
+for (const [fileCount, directoryCount] of [
+  [100, 0],
+  [1000, 0],
+  [5000, 0],
+  [5000, 5],
+  [0, 100]
+]) {
+  const nodes = Array.from({ length: fileCount + directoryCount }, (_, index) => ({
+    name: `item-${index}`,
+    path: `/repo/item-${index}`,
+    relativePath: `item-${index}`,
+    isDirectory: index >= fileCount,
+    depth: 0
+  }))
+  const expected = original(nodes)
+  const actual = selectDeletionRoots(nodes)
+  assert.equal(actual.length, expected.length)
+  actual.forEach((node, index) => assert.equal(node, expected[index]))
+  results.push({
+    fileCount,
+    directoryCount,
+    beforeMs: measure(original, nodes),
+    afterMs: measure(selectDeletionRoots, nodes)
+  })
+}
+console.log(JSON.stringify({ node: process.version, platform: process.platform, results }, null, 2))
diff --git a/src/renderer/src/components/right-sidebar/file-explorer-batch-deletion.test.ts b/src/renderer/src/components/right-sidebar/file-explorer-batch-deletion.test.ts
index e93928bf4fd..688683bce13 100644
--- a/src/renderer/src/components/right-sidebar/file-explorer-batch-deletion.test.ts
+++ b/src/renderer/src/components/right-sidebar/file-explorer-batch-deletion.test.ts
@@ -37,6 +37,66 @@ describe('selectDeletionRoots', () => {
     const other = node('/repo/a.ts/impossible-child')
     expect(selectDeletionRoots([file, other])).toEqual([file, other])
   })
+
+  it('reads directory membership once per selected node, including file-only selections', () => {
+    let directoryReads = 0
+    const nodes = Array.from({ length: 1_000 }, (_, index) => ({
+      ...node(`/repo/file-${index}.ts`),
+      get isDirectory() {
+        directoryReads += 1
+        return false
+      }
+    }))
+    const selected = selectDeletionRoots(nodes)
+    expect(directoryReads).toBe(nodes.length)
+    expect(selected).not.toBe(nodes)
+    selected.forEach((entry, index) => expect(entry).toBe(nodes[index]))
+  })
+
+  it('preserves order, node identity and host ownership when children precede parents', () => {
+    const child = node('/repo/docs/guide.md')
+    const first = { ...node('/repo/first.ts'), operationOwner: { kind: 'local' as const } }
+    const parent = {
+      ...node('/repo/docs', true),
+      operationOwner: { kind: 'ssh' as const, connectionId: 'ssh-owner' }
+    }
+    const last = {
+      ...node('/repo/last.ts'),
+      operationOwner: { kind: 'unresolved' as const }
+    }
+    const nodes = [child, first, parent, last]
+    const selected = selectDeletionRoots(nodes)
+    expect(selected).toEqual([first, parent, last])
+    expect(selected[0]).toBe(first)
+    expect(selected[1]).toBe(parent)
+    expect(selected[2]).toBe(last)
+    expect(nodes).toEqual([child, first, parent, last])
+  })
+
+  it('keeps repeated references but excludes distinct directories with the same path', () => {
+    const dir = node('/repo/docs', true)
+    expect(selectDeletionRoots([dir, dir])).toEqual([dir, dir])
+    expect(selectDeletionRoots([dir, { ...dir }])).toEqual([])
+    const file = node('/repo/docs')
+    expect(selectDeletionRoots([file, dir])).toEqual([dir])
+  })
+
+  it.each([
+    ['/repo/docs/', '/repo/docs/guide.md', '/repo/docs-other/guide.md'],
+    ['C:\\Repo\\Docs\\', 'c:/repo/docs/guide.md', 'C:/Repo/Docs-other/guide.md'],
+    ['\\\\Server\\Share\\Docs', '//server/share/docs/guide.md', '//server/other/docs/guide.md']
+  ])('retains path boundaries for %s', (parentPath, childPath, outsidePath) => {
+    const parent = node(parentPath, true)
+    const child = node(childPath)
+    const outside = node(outsidePath)
+    expect(selectDeletionRoots([outside, child, parent])).toEqual([outside, parent])
+  })
+
+  it('keeps case-distinct POSIX paths', () => {
+    const parent = node('/repo/Docs', true)
+    const outside = node('/repo/docs/guide.md')
+    expect(selectDeletionRoots([outside, parent])).toEqual([outside, parent])
+  })
 })
 
 describe('runBatchDeletion', () => {
diff --git a/src/renderer/src/components/right-sidebar/file-explorer-batch-deletion.ts b/src/renderer/src/components/right-sidebar/file-explorer-batch-deletion.ts
index 63a5d029739..5f052bec588 100644
--- a/src/renderer/src/components/right-sidebar/file-explorer-batch-deletion.ts
+++ b/src/renderer/src/components/right-sidebar/file-explorer-batch-deletion.ts
@@ -5,11 +5,9 @@ import type { TreeNode } from './file-explorer-types'
 // already removes the child, and issuing both requests races on the
 // now-missing path and produces spurious errors.
 export function selectDeletionRoots(nodes: TreeNode[]): TreeNode[] {
+  const directories = nodes.filter((node) => node.isDirectory)
   return nodes.filter(
-    (n) =>
-      !nodes.some(
-        (other) => other !== n && other.isDirectory && isPathEqualOrDescendant(n.path, other.path)
-      )
+    (n) => !directories.some((other) => other !== n && isPathEqualOrDescendant(n.path, other.path))
   )
 }