diff --git a/apps/sim/connectors/jira/jira.ts b/apps/sim/connectors/jira/jira.ts
index a044e75d1..9713f0dc9 100644
--- a/apps/sim/connectors/jira/jira.ts
+++ b/apps/sim/connectors/jira/jira.ts
@@ -140,9 +140,10 @@ export const jiraConnector: ConnectorConfig = {
 
     const cloudId = await getJiraCloudId(domain, accessToken)
 
-    let jql = `project = ${projectKey} ORDER BY updated DESC`
+    const safeKey = projectKey.replace(/\\/g, '\\\\').replace(/"/g, '\\"')
+    let jql = `project = "${safeKey}" ORDER BY updated DESC`
     if (jqlFilter.trim()) {
-      jql = `project = ${projectKey} AND (${jqlFilter.trim()}) ORDER BY updated DESC`
+      jql = `project = "${safeKey}" AND (${jqlFilter.trim()}) ORDER BY updated DESC`
     }
 
     const startAt = cursor ? Number(cursor) : 0
@@ -250,7 +251,8 @@ export const jiraConnector: ConnectorConfig = {
       const cloudId = await getJiraCloudId(domain, accessToken)
 
       const params = new URLSearchParams()
-      params.append('jql', `project = ${projectKey}`)
+      const safeKey = projectKey.replace(/\\/g, '\\\\').replace(/"/g, '\\"')
+      params.append('jql', `project = "${safeKey}"`)
       params.append('maxResults', '0')
 
       const url = `https://api.atlassian.com/ex/jira/${cloudId}/rest/api/3/search?${params.toString()}`
diff --git a/apps/sim/lib/knowledge/connectors/sync-engine.ts b/apps/sim/lib/knowledge/connectors/sync-engine.ts
index 61c040184..afbfd55f4 100644
--- a/apps/sim/lib/knowledge/connectors/sync-engine.ts
+++ b/apps/sim/lib/knowledge/connectors/sync-engine.ts
@@ -192,7 +192,13 @@ export async function executeSync(
     const excludedDocs = await db
       .select({ externalId: document.externalId })
       .from(document)
-      .where(and(eq(document.connectorId, connectorId), eq(document.userExcluded, true)))
+      .where(
+        and(
+          eq(document.connectorId, connectorId),
+          eq(document.userExcluded, true),
+          isNull(document.deletedAt)
+        )
+      )
 
     const excludedExternalIds = new Set(excludedDocs.map((d) => d.externalId).filter(Boolean))