diff --git a/services/github/pod-github/src/sync/issueBase.ts b/services/github/pod-github/src/sync/issueBase.ts
index 73f49cf34d..f2e9c9278a 100644
--- a/services/github/pod-github/src/sync/issueBase.ts
+++ b/services/github/pod-github/src/sync/issueBase.ts
@@ -628,9 +628,17 @@ export abstract class IssueSyncManagerBase {
             itemId: target.prjData?.id as string
           })
         } catch (err: any) {
+          if (err.errors?.[0]?.type === 'NOT_FOUND') {
+            errors.push({ error: err, response })
+            return errors
+          }
           Analytics.handleError(err)
           // Failed to update one particular value, skip it.
-          this.ctx.error('error during field update', { error: err, response })
+          this.ctx.error('error during field update', {
+            error: err,
+            response,
+            workspace: this.provider.getWorkspaceId().name
+          })
           errors.push({ error: err, response })
         }
       }
@@ -892,10 +900,9 @@ export abstract class IssueSyncManagerBase {
       }
       if (fieldsUpdate.length > 0 && syncToProject && target.prjData !== undefined) {
         const errors = await this.updateIssueValues(target, okit, fieldsUpdate)
-        if (errors.length > 0) {
-          return { externalVersion: '', needUpdate: githubSyncVersion, error: errors }
+        if (errors.length === 0) {
+          needExternalSync = true
         }
-        needExternalSync = true
       }
       // TODO: Add support for labels, milestone, assignees
     }
diff --git a/services/github/pod-github/src/sync/pullrequests.ts b/services/github/pod-github/src/sync/pullrequests.ts
index b8885f5809..8ef9fd275d 100644
--- a/services/github/pod-github/src/sync/pullrequests.ts
+++ b/services/github/pod-github/src/sync/pullrequests.ts
@@ -971,6 +971,10 @@ export class PullRequestSyncManager extends IssueSyncManagerBase implements DocS
       return { needSync: githubSyncVersion }
     }
 
+    if (info.repository == null) {
+      return { needSync: githubSyncVersion }
+    }
+
     const pullRequestExternal = info.external as unknown as PullRequestExternalData
 
     if (info.externalVersion !== githubExternalSyncVersion) {
diff --git a/services/github/pod-github/src/sync/repository.ts b/services/github/pod-github/src/sync/repository.ts
index bafaf1d542..998cd08006 100644
--- a/services/github/pod-github/src/sync/repository.ts
+++ b/services/github/pod-github/src/sync/repository.ts
@@ -265,7 +265,14 @@ export class RepositorySyncMapper implements DocSyncManager {
 
     let allRepos: GithubIntegrationRepository[] = [...allRepositories]
 
+    const githubRepos:
+    | Repository
+    | Endpoints['GET /installation/repositories']['response']['data']['repositories'][0][] = []
     for await (const { repository } of iterable) {
+      githubRepos.push(repository)
+    }
+
+    for (const repository of githubRepos) {
       const integrationRepo: GithubIntegrationRepository | undefined = allRepos.find(
         (it) => it.repositoryId === repository.id
       )
@@ -325,13 +332,8 @@ export class RepositorySyncMapper implements DocSyncManager {
 
     // Ok we have repos removed from integration, we need to delete them.
     for (const repo of allRepos) {
-      await this.client.remove(repo)
-      const prj = projects.find((it) => it._id === repo.githubProject)
-      if (prj !== undefined) {
-        await this.client.update(prj, {
-          $pull: { repositories: repo._id }
-        })
-      }
+      // Mark as archived
+      await this.client.update(repo, { archived: true })
     }
 
     // We need to delete and disconnect missing repositories.
diff --git a/services/github/pod-github/src/worker.ts b/services/github/pod-github/src/worker.ts
index 473822d6bd..db5f974876 100644
--- a/services/github/pod-github/src/worker.ts
+++ b/services/github/pod-github/src/worker.ts
@@ -395,9 +395,6 @@ export class GithubWorker implements IntegrationManager {
   periodicSyncPromise: Promise<void> | undefined
   async performPeriodicSync (): Promise<void> {
     try {
-      for (const inst of this.integrations.values()) {
-        await this.repositoryManager.reloadRepositories(inst)
-      }
       this.triggerUpdate()
     } catch (err: any) {
       Analytics.handleError(err)