diff --git a/packages/server/src/appMigrations/migrations/20240604153647_initial_sqs.ts b/packages/server/src/appMigrations/migrations/20240604153647_initial_sqs.ts
index 05174b8cf1..6ad3c09c3c 100644
--- a/packages/server/src/appMigrations/migrations/20240604153647_initial_sqs.ts
+++ b/packages/server/src/appMigrations/migrations/20240604153647_initial_sqs.ts
@@ -17,15 +17,17 @@ const migration = async () => {
 
     // it already has the junction table ID - no need to migrate
     if (!linkDoc.tableId) {
-      linkDoc.tableId = new LinkDocumentImpl(
+      const newLink = new LinkDocumentImpl(
         linkDoc.doc1.tableId,
         linkDoc.doc1.fieldName,
         linkDoc.doc1.rowId,
         linkDoc.doc2.tableId,
         linkDoc.doc2.fieldName,
         linkDoc.doc2.rowId
-      ).tableId
-      docsToUpdate.push(linkDoc)
+      )
+      newLink._id = linkDoc._id!
+      newLink._rev = linkDoc._rev
+      docsToUpdate.push(newLink)
     }
   }
 
diff --git a/packages/server/src/appMigrations/migrations/tests/20240604153647_initial_sqs.spec.ts b/packages/server/src/appMigrations/migrations/tests/20240604153647_initial_sqs.spec.ts
new file mode 100644
index 0000000000..64420d239f
--- /dev/null
+++ b/packages/server/src/appMigrations/migrations/tests/20240604153647_initial_sqs.spec.ts
@@ -0,0 +1,116 @@
+import * as setup from "../../../api/routes/tests/utilities"
+import { basicTable } from "../../../tests/utilities/structures"
+import {
+  db as dbCore,
+  SQLITE_DESIGN_DOC_ID,
+  context,
+} from "@budibase/backend-core"
+import {
+  LinkDocument,
+  DocumentType,
+  SQLiteDefinition,
+  SQLiteType,
+} from "@budibase/types"
+import {
+  generateJunctionTableID,
+  generateLinkID,
+  generateRowID,
+} from "../../../db/utils"
+import migration from "../20240604153647_initial_sqs"
+
+const config = setup.getConfig()
+let tableId: string
+
+function oldLinkDocInfo() {
+  const tableId1 = `${DocumentType.TABLE}_a`,
+    tableId2 = `${DocumentType.TABLE}_b`
+  return {
+    tableId1,
+    tableId2,
+    rowId1: generateRowID(tableId1, "b"),
+    rowId2: generateRowID(tableId2, "a"),
+    col1: "columnB",
+    col2: "columnA",
+  }
+}
+
+function oldLinkDocID() {
+  const { tableId1, tableId2, rowId1, rowId2, col1, col2 } = oldLinkDocInfo()
+  return generateLinkID(tableId1, tableId2, rowId1, rowId2, col1, col2)
+}
+
+function oldLinkDocument(): Omit<LinkDocument, "tableId"> {
+  const { tableId1, tableId2, rowId1, rowId2, col1, col2 } = oldLinkDocInfo()
+  return {
+    type: "link",
+    _id: oldLinkDocID(),
+    doc1: {
+      tableId: tableId1,
+      fieldName: col1,
+      rowId: rowId1,
+    },
+    doc2: {
+      tableId: tableId2,
+      fieldName: col2,
+      rowId: rowId2,
+    },
+  }
+}
+
+async function sqsDisabled(cb: () => Promise<void>) {
+  await config.withEnv({ SQS_SEARCH_ENABLE: "" }, cb)
+}
+
+async function sqsEnabled(cb: () => Promise<void>) {
+  await config.withEnv({ SQS_SEARCH_ENABLE: "1" }, cb)
+}
+
+beforeAll(async () => {
+  await sqsDisabled(async () => {
+    await config.init()
+    const table = await config.api.table.save(basicTable())
+    tableId = table._id!
+    const db = dbCore.getDB(config.appId!)
+    // old link document
+    await db.put(oldLinkDocument())
+  })
+})
+
+describe("SQS migration", () => {
+  it("test migration runs as expected against an older DB", async () => {
+    const db = dbCore.getDB(config.appId!)
+    // confirm nothing exists initially
+    await sqsDisabled(async () => {
+      let error: any | undefined
+      try {
+        await db.get(SQLITE_DESIGN_DOC_ID)
+      } catch (err: any) {
+        error = err
+      }
+      expect(error).toBeDefined()
+      expect(error.status).toBe(404)
+    })
+    await sqsEnabled(async () => {
+      await context.doInAppContext(config.appId!, async () => {
+        await migration()
+      })
+      const designDoc = await db.get<SQLiteDefinition>(SQLITE_DESIGN_DOC_ID)
+      expect(designDoc.sql.tables).toBeDefined()
+      const mainTableDef = designDoc.sql.tables[tableId]
+      expect(mainTableDef).toBeDefined()
+      expect(mainTableDef.fields.name).toEqual(SQLiteType.TEXT)
+      expect(mainTableDef.fields.description).toEqual(SQLiteType.TEXT)
+
+      const { tableId1, tableId2, rowId1, rowId2 } = oldLinkDocInfo()
+      const linkDoc = await db.get<LinkDocument>(oldLinkDocID())
+      expect(linkDoc.tableId).toEqual(
+        generateJunctionTableID(tableId1, tableId2)
+      )
+      // should have swapped the documents
+      expect(linkDoc.doc1.tableId).toEqual(tableId2)
+      expect(linkDoc.doc1.rowId).toEqual(rowId2)
+      expect(linkDoc.doc2.tableId).toEqual(tableId1)
+      expect(linkDoc.doc2.rowId).toEqual(rowId1)
+    })
+  })
+})
diff --git a/packages/server/src/environment.ts b/packages/server/src/environment.ts
index 2c91f1cb48..b44d7547a2 100644
--- a/packages/server/src/environment.ts
+++ b/packages/server/src/environment.ts
@@ -96,6 +96,7 @@ const environment = {
   DISABLE_THREADING: process.env.DISABLE_THREADING,
   DISABLE_AUTOMATION_LOGS: process.env.DISABLE_AUTOMATION_LOGS,
   DISABLE_RATE_LIMITING: process.env.DISABLE_RATE_LIMITING,
+  DISABLE_APP_MIGRATIONS: process.env.SKIP_APP_MIGRATIONS || false,
   MULTI_TENANCY: process.env.MULTI_TENANCY,
   ENABLE_ANALYTICS: process.env.ENABLE_ANALYTICS,
   SELF_HOSTED: process.env.SELF_HOSTED,
diff --git a/packages/server/src/middleware/appMigrations.ts b/packages/server/src/middleware/appMigrations.ts
index fdaeb3a03d..6ad356427b 100644
--- a/packages/server/src/middleware/appMigrations.ts
+++ b/packages/server/src/middleware/appMigrations.ts
@@ -1,13 +1,13 @@
 import { UserCtx } from "@budibase/types"
 import { checkMissingMigrations } from "../appMigrations"
-import { env } from "@budibase/backend-core"
+import env from "../environment"
 
 export default async (ctx: UserCtx, next: any) => {
   const { appId } = ctx
 
   // migrations can be disabled via environment variable if you
   // need to completely disable migrations, e.g. for testing
-  if (env.SKIP_APP_MIGRATIONS) {
+  if (env.DISABLE_APP_MIGRATIONS) {
     return next()
   }