diff --git a/lib/ops/message-store-ops.js b/lib/ops/message-store-ops.js
--- a/lib/ops/message-store-ops.js
+++ b/lib/ops/message-store-ops.js
@@ -1,6 +1,7 @@
 // @flow
 
 import { type BaseStoreOpsHandlers } from './base-ops.js';
+import { threadSpecs } from '../shared/threads/thread-specs.js';
 import type {
   ClientDBMessageInfo,
   ClientDBThreadMessageInfo,
@@ -10,6 +11,7 @@
   LocalMessageInfo,
   ClientDBLocalMessageInfo,
 } from '../types/message-types.js';
+import { type MixedRawThreadInfos } from '../types/thread-types.js';
 import {
   translateClientDBMessageInfoToRawMessageInfo,
   translateRawMessageInfoToClientDBMessageInfo,
@@ -29,7 +31,7 @@
 
 export type ReplaceMessageOperation = {
   +type: 'replace',
-  +payload: { +id: string, +messageInfo: RawMessageInfo },
+  +payload: { +id: string, +messageInfo: RawMessageInfo, +isBackedUp: boolean },
 };
 
 export type RekeyMessageOperation = {
@@ -112,7 +114,7 @@
   | RemoveMessageStoreLocalMessageInfosOperation
   | RemoveMessageStoreAllLocalMessageInfosOperation;
 
-export const messageStoreOpsHandlers: BaseStoreOpsHandlers<
+const messageStoreOpsHandlers: BaseStoreOpsHandlers<
   MessageStore,
   MessageStoreOperation,
   ClientDBMessageStoreOperation,
@@ -246,3 +248,27 @@
     );
   },
 };
+
+function createReplaceMessageOperation(
+  id: string,
+  messageInfo: RawMessageInfo,
+  threadInfos: MixedRawThreadInfos,
+): ReplaceMessageOperation {
+  const threadInfo = threadInfos[messageInfo.threadID];
+  if (!threadInfo) {
+    return {
+      type: 'replace',
+      payload: { id, messageInfo, isBackedUp: true },
+    };
+  }
+  return {
+    type: 'replace',
+    payload: {
+      id,
+      messageInfo,
+      isBackedUp: threadSpecs[threadInfo.type].protocol.dataIsBackedUp,
+    },
+  };
+}
+
+export { messageStoreOpsHandlers, createReplaceMessageOperation };
diff --git a/lib/reducers/message-reducer.js b/lib/reducers/message-reducer.js
--- a/lib/reducers/message-reducer.js
+++ b/lib/reducers/message-reducer.js
@@ -61,8 +61,8 @@
 import {
   messageStoreOpsHandlers,
   type MessageStoreOperation,
-  type ReplaceMessageOperation,
   type ReplaceMessageStoreLocalMessageInfoOperation,
+  createReplaceMessageOperation,
 } from '../ops/message-store-ops.js';
 import { pendingToRealizedThreadIDsSelector } from '../selectors/thread-selectors.js';
 import {
@@ -174,11 +174,12 @@
   const orderedMessageInfos = sortMessageInfoList(unshimmed);
   const messages = _keyBy(messageID)(orderedMessageInfos);
 
-  const messageStoreReplaceOperations = orderedMessageInfos.map(
-    messageInfo => ({
-      type: 'replace',
-      payload: { id: messageID(messageInfo), messageInfo },
-    }),
+  const messageStoreReplaceOperations = orderedMessageInfos.map(messageInfo =>
+    createReplaceMessageOperation(
+      messageID(messageInfo),
+      messageInfo,
+      threadInfos,
+    ),
   );
 
   const threadsToMessageIDs =
@@ -260,11 +261,11 @@
       continue;
     }
 
-    const updateMsgOperation: ReplaceMessageOperation = {
-      type: 'replace',
-      payload: { id: storeMessageID, messageInfo: messages[storeMessageID] },
-    };
-
+    const updateMsgOperation = createReplaceMessageOperation(
+      storeMessageID,
+      messages[storeMessageID],
+      threadInfos,
+    );
     messageStoreOperations.push(updateMsgOperation);
   }
 
@@ -603,10 +604,9 @@
 
   const newMessages = _keyBy(messageID)(orderedNewMessageInfos);
   for (const id in newMessages) {
-    newMessageOps.push({
-      type: 'replace',
-      payload: { id, messageInfo: newMessages[id] },
-    });
+    newMessageOps.push(
+      createReplaceMessageOperation(id, newMessages[id], threadInfos),
+    );
   }
 
   if (localIDsToServerIDs.size > 0) {
@@ -1119,10 +1119,7 @@
     }
 
     const messageStoreOperations: MessageStoreOperation[] = [
-      {
-        type: 'replace',
-        payload: { id: localID, messageInfo: payload },
-      },
+      createReplaceMessageOperation(localID, payload, newThreadInfos),
     ];
 
     let updatedThreads;
@@ -1304,10 +1301,13 @@
       time: payload.time,
     };
     newMessages[payload.serverID] = newMessage;
-    messageStoreOperations.push({
-      type: 'replace',
-      payload: { id: payload.serverID, messageInfo: newMessage },
-    });
+    messageStoreOperations.push(
+      createReplaceMessageOperation(
+        payload.serverID,
+        newMessage,
+        newThreadInfos,
+      ),
+    );
     const threadID = payload.threadID;
     const newMessageIDs = _flow(
       _uniq,
@@ -1642,13 +1642,7 @@
     );
 
     const messageStoreOperations = [
-      {
-        type: 'replace',
-        payload: {
-          id,
-          messageInfo: updatedMessage,
-        },
-      },
+      createReplaceMessageOperation(id, updatedMessage, newThreadInfos),
     ];
 
     const processedMessageStore = processMessageStoreOperations(
@@ -1685,10 +1679,7 @@
         };
 
     const messageStoreOperations = [
-      {
-        type: 'replace',
-        payload: { id: localID, messageInfo },
-      },
+      createReplaceMessageOperation(localID, messageInfo, newThreadInfos),
       {
         type: 'replace_threads',
         payload: {
diff --git a/native/redux/unshim-utils.js b/native/redux/unshim-utils.js
--- a/native/redux/unshim-utils.js
+++ b/native/redux/unshim-utils.js
@@ -1,9 +1,11 @@
 // @flow
 
 import {
+  createReplaceMessageOperation,
   type MessageStoreOperation,
   messageStoreOpsHandlers,
 } from 'lib/ops/message-store-ops.js';
+import { threadStoreOpsHandlers } from 'lib/ops/thread-store-ops.js';
 import { messageID } from 'lib/shared/id-utils.js';
 import { unshimFunc } from 'lib/shared/unshim-utils.js';
 import { type MessageType } from 'lib/types/message-types-enum.js';
@@ -24,10 +26,14 @@
   unshimTypes: $ReadOnlyArray<MessageType>,
   handleMigrationFailure?: AppState => AppState,
 ): MigrationResult<AppState> {
-  // 1. Get messages from SQLite `messages` table.
+  // 1. Get threads and messages from SQLite `threads` and `messages` tables.
+  const clientDBThreadInfos = commCoreModule.getAllThreadsSync();
   const clientDBMessageInfos = commCoreModule.getInitialMessagesSync();
 
-  // 2. Translate `ClientDBMessageInfo`s to `RawMessageInfo`s.
+  // 2. Translate `ClientDBThreadInfo`s to `RawThreadInfo`s and
+  //    `ClientDBMessageInfo`s to `RawMessageInfo`s.
+  const rawThreadInfos =
+    threadStoreOpsHandlers.translateClientDBData(clientDBThreadInfos);
   const rawMessageInfos = clientDBMessageInfos.map(
     translateClientDBMessageInfoToRawMessageInfo,
   );
@@ -43,10 +49,13 @@
     {
       type: 'remove_all',
     },
-    ...unshimmedRawMessageInfos.map((message: RawMessageInfo) => ({
-      type: 'replace',
-      payload: { id: messageID(message), messageInfo: message },
-    })),
+    ...unshimmedRawMessageInfos.map((message: RawMessageInfo) =>
+      createReplaceMessageOperation(
+        messageID(message),
+        message,
+        rawThreadInfos,
+      ),
+    ),
   ];
 
   // 5. Try processing `ClientDBMessageStoreOperation`s and log out if
diff --git a/web/redux/initial-state-gate.js b/web/redux/initial-state-gate.js
--- a/web/redux/initial-state-gate.js
+++ b/web/redux/initial-state-gate.js
@@ -182,7 +182,10 @@
           messageStoreOperations = [
             ...entries(messages).map(([id, messageInfo]) => ({
               type: 'replace',
-              payload: { id, messageInfo },
+              // This code is responsible for migrating keyserver messages to
+              // SQLite, which means this data shouldn't be included in the
+              // backup because it is owned by keyserver.
+              payload: { id, messageInfo, isBackedUp: false },
             })),
             {
               type: 'replace_threads',
diff --git a/web/redux/unshim-utils.js b/web/redux/unshim-utils.js
--- a/web/redux/unshim-utils.js
+++ b/web/redux/unshim-utils.js
@@ -1,16 +1,19 @@
 // @flow
 
 import {
+  createReplaceMessageOperation,
   type MessageStoreOperation,
   messageStoreOpsHandlers,
 } from 'lib/ops/message-store-ops.js';
 import { messageID } from 'lib/shared/id-utils.js';
 import { unshimFunc } from 'lib/shared/unshim-utils.js';
+import { databaseIdentifier } from 'lib/types/database-identifier-types.js';
 import { type MessageType } from 'lib/types/message-types-enum.js';
 import type {
   RawMessageInfo,
   ClientDBMessageInfo,
 } from 'lib/types/message-types.js';
+import { getConfig } from 'lib/utils/config.js';
 import { translateClientDBMessageInfoToRawMessageInfo } from 'lib/utils/message-ops-utils.js';
 import type { MigrationResult } from 'lib/utils/migration-utils.js';
 
@@ -39,12 +42,11 @@
   }
 
   // 2. Get existing `stores` from SQLite.
-  const stores = await sharedWorker.schedule({
-    type: workerRequestMessageTypes.GET_CLIENT_STORE,
-  });
+  const clientStore = await getConfig().sqliteAPI.getClientDBStore(
+    databaseIdentifier.MAIN,
+  );
 
-  const messages: ?$ReadOnlyArray<ClientDBMessageInfo> =
-    stores?.store?.messages;
+  const messages: ?$ReadOnlyArray<ClientDBMessageInfo> = clientStore?.messages;
 
   if (messages === null || messages === undefined || messages.length === 0) {
     return {
@@ -69,10 +71,13 @@
     {
       type: 'remove_all',
     },
-    ...unshimmedRawMessageInfos.map((message: RawMessageInfo) => ({
-      type: 'replace',
-      payload: { id: messageID(message), messageInfo: message },
-    })),
+    ...unshimmedRawMessageInfos.map((message: RawMessageInfo) =>
+      createReplaceMessageOperation(
+        messageID(message),
+        message,
+        clientStore?.threadStore?.threadInfos ?? {},
+      ),
+    ),
   ];
 
   // 6. Process the constructed `messageStoreOperations`.