diff --git a/src/utilities/manifest.ts b/src/utilities/manifest.ts
index c9bac25..60cca13 100644
--- a/src/utilities/manifest.ts
+++ b/src/utilities/manifest.ts
@@ -86,36 +86,6 @@ export async function generateManifestFiles(
     }
   }
 
-  for (const node of themeNodes) {
-    // Add theme nodes not present in the old import map
-    // They have been added manually by the user since the last time the import map was generated
-    if ((node.type === 'snippet' || node.type === 'asset') && !oldFilesMap[node.themeFolder]?.[node.name]) {
-        const collectionNode = collectionNodes.find(n => n.themeFolder === node.themeFolder && n.name === node.name)
-
-        if (collectionNode) {
-          if (options.ignoreConflicts) {
-            // If the user has passed the --ignore-conflicts flag, skip the node so it can be logged later as a component entry
-            continue;
-          } else {
-            // If the node also exists in the collection, warn the user of the potential conflict but keep as a @theme entry
-            newFilesMap[node.themeFolder][node.name] = '@theme'
-            logger.log(`Conflict Warning: Pre-existing file ${node.themeFolder}/${node.name} without mapping conflicts with file in ${collectionName}. Keeping the theme file.`)
-          }
-        } else {
-          // If the node does not exist in the collection, add it to the new import map as a @theme entry
-          newFilesMap[node.themeFolder][node.name] = '@theme'
-        }
-      }
-
-    // Persist prexisting asset entries from @theme or other collections
-    if (node.type === 'asset') {
-      const oldImportMapValue = oldFilesMap[node.themeFolder]?.[node.name]
-      if (oldImportMapValue !== collectionName && typeof oldImportMapValue === 'string') {
-        newFilesMap[node.themeFolder][node.name] = oldImportMapValue
-      }
-    }
-  }
-
   function addFilesMapEntry(themeFolder: LiquidNode['themeFolder'], name: string) {
     const oldImportMapValue = oldFilesMap[themeFolder]?.[name]
     const newImportMapValue = newFilesMap[themeFolder]?.[name]
@@ -184,5 +154,44 @@ export async function generateManifestFiles(
     }
   }
 
+  for (const node of themeNodes) {
+    // Add theme nodes not present in the old import map
+    // They have been added manually by the user since the last time the import map was generated
+    if ((node.type === 'snippet' || node.type === 'asset') && !oldFilesMap[node.themeFolder]?.[node.name]) {
+        const collectionNode = collectionNodes.find(n => n.themeFolder === node.themeFolder && n.name === node.name)
+
+        if (collectionNode) {
+          if (options.ignoreConflicts) {
+            // If the user has passed the --ignore-conflicts flag, skip the node so it can be logged later as a component entry
+            continue;
+          } else {
+            // If the node also exists in the collection, warn the user of the potential conflict but keep as a @theme entry
+            newFilesMap[node.themeFolder][node.name] = '@theme'
+            logger.log(`Conflict Warning: Pre-existing file ${node.themeFolder}/${node.name} without mapping conflicts with file in ${collectionName}. Keeping the theme file.`)
+          }
+        } else {
+          // If the node does not exist in the collection, add it to the new import map as a @theme entry
+          newFilesMap[node.themeFolder][node.name] = '@theme'
+        }
+      }
+
+    // Persist prexisting asset entries from @theme or other collections
+    if (node.type === 'asset') {
+      const oldImportMapValue = oldFilesMap[node.themeFolder]?.[node.name]
+      if (oldImportMapValue !== collectionName && typeof oldImportMapValue === 'string') {
+        newFilesMap[node.themeFolder][node.name] = oldImportMapValue
+      }
+    }
+
+    // Persist prexisting snippet entries from @theme or other collections
+    if (node.type === 'snippet') {
+      const oldImportMapValue = oldFilesMap[node.themeFolder]?.[node.name]
+      const newImportMapValue = newFilesMap[node.themeFolder]?.[node.name]
+      if (newImportMapValue === undefined && oldImportMapValue !== collectionName && typeof oldImportMapValue === 'string') {
+        newFilesMap[node.themeFolder][node.name] = oldImportMapValue
+      }
+    }
+  }
+
   return newFilesMap
 }
\ No newline at end of file
diff --git a/test/commands/theme/component/map.test.ts b/test/commands/theme/component/map.test.ts
index 4f06d27..153b3ba 100644
--- a/test/commands/theme/component/map.test.ts
+++ b/test/commands/theme/component/map.test.ts
@@ -76,6 +76,18 @@ describe('theme component map', () => {
     expect(data.files.snippets['include-tag.liquid']).to.equal('@theme') // Should work with include tag
   })
 
+  it('persists entries that are associated with @theme or another collection in the manifest', async () => {
+    const beforeData = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
+    expect(beforeData.files.snippets['unreferenced-theme-snippet.liquid']).to.equal('@theme')
+    expect(beforeData.files.snippets['unreferenced-other-collection-snippet.liquid']).to.equal('@other/collection')
+
+    await runCommand(['theme', 'component', 'map', testThemePath])
+
+    const data = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
+    expect(data.files.snippets['unreferenced-theme-snippet.liquid']).to.equal('@theme')
+    expect(data.files.snippets['unreferenced-other-collection-snippet.liquid']).to.equal('@other/collection')
+  })
+
   it('adds entries for newly referenced components from current collection', async () => {
     const beforeData = JSON.parse(fs.readFileSync(path.join(testThemePath, 'component.manifest.json'), 'utf8'))
     expect(beforeData.files.snippets['new.liquid']).to.be.undefined
diff --git a/test/fixtures/theme/component.manifest.json b/test/fixtures/theme/component.manifest.json
index 6470e32..2fb5e4a 100644
--- a/test/fixtures/theme/component.manifest.json
+++ b/test/fixtures/theme/component.manifest.json
@@ -16,7 +16,9 @@
       "to-be-copied.liquid": "@archetype-themes/test-collection",
       "to-be-copied-snippet.liquid": "@archetype-themes/test-collection",
       "existing-subfolder.liquid": "@theme",
-      "removed-subfolder.liquid": "@theme"
+      "removed-subfolder.liquid": "@theme",
+      "unreferenced-theme-snippet.liquid": "@theme",
+      "unreferenced-other-collection-snippet.liquid": "@other/collection"
     },
     "assets": {
       "other-collection-component.css": "@other/collection",
diff --git a/test/fixtures/theme/snippets/unreferenced-other-collection-snippet.liquid b/test/fixtures/theme/snippets/unreferenced-other-collection-snippet.liquid
new file mode 100644
index 0000000..e69de29
diff --git a/test/fixtures/theme/snippets/unreferenced-theme-snippet.liquid b/test/fixtures/theme/snippets/unreferenced-theme-snippet.liquid
new file mode 100644
index 0000000..e69de29