diff --git a/src/interface/obsidian/src/search_modal.ts b/src/interface/obsidian/src/search_modal.ts
index e99e644e..9fd1ac65 100644
--- a/src/interface/obsidian/src/search_modal.ts
+++ b/src/interface/obsidian/src/search_modal.ts
@@ -161,7 +161,7 @@ export class KhojSearchModal extends SuggestModal<SearchResult> {
         // Open vault file at heading of chosen search result
         if (file_match) {
             let resultHeading = file_match.extension !== 'pdf' ? result.entry.split('\n', 1)[0] : '';
-            let linkToEntry = `${file_match.path}${resultHeading}`
+            let linkToEntry = resultHeading.startsWith('#') ? `${file_match.path}${resultHeading}` : file_match.path;
             this.app.workspace.openLinkText(linkToEntry, '');
             console.log(`Link: ${linkToEntry}, File: ${file_match.path}, Heading: ${resultHeading}`);
         }
diff --git a/src/interface/obsidian/src/utils.ts b/src/interface/obsidian/src/utils.ts
index 053562b6..c14912e5 100644
--- a/src/interface/obsidian/src/utils.ts
+++ b/src/interface/obsidian/src/utils.ts
@@ -72,41 +72,58 @@ export async function configureKhojBackend(vault: Vault, setting: KhojSetting, n
                 }
             }
             // Else if khoj is not configured to index markdown files in configured obsidian vault
-            else if (data["content-type"]["markdown"]["input-filter"].length != 1 ||
+            else if (
+                data["content-type"]["markdown"]["input-files"] != null ||
+                data["content-type"]["markdown"]["input-filter"] == null ||
+                data["content-type"]["markdown"]["input-filter"].length != 1 ||
                 data["content-type"]["markdown"]["input-filter"][0] !== mdInVault) {
-                // Update markdown config in khoj content-type config
-                // Set markdown config to only index markdown files in configured obsidian vault
-                let khojMdIndexDirectory = getIndexDirectoryFromBackendConfig(data["content-type"]["markdown"]["embeddings-file"]);
-                data["content-type"]["markdown"] = {
-                    "input-filter": [mdInVault],
-                    "input-files": null,
-                    "embeddings-file": `${khojMdIndexDirectory}/${indexName}.pt`,
-                    "compressed-jsonl": `${khojMdIndexDirectory}/${indexName}.jsonl.gz`,
-                }
+                    // Update markdown config in khoj content-type config
+                    // Set markdown config to only index markdown files in configured obsidian vault
+                    let khojMdIndexDirectory = getIndexDirectoryFromBackendConfig(data["content-type"]["markdown"]["embeddings-file"]);
+                    data["content-type"]["markdown"] = {
+                        "input-filter": [mdInVault],
+                        "input-files": null,
+                        "embeddings-file": `${khojMdIndexDirectory}/${indexName}.pt`,
+                        "compressed-jsonl": `${khojMdIndexDirectory}/${indexName}.jsonl.gz`,
+                    }
             }
 
             if (khoj_already_configured && !data["content-type"]["pdf"]) {
-                // Add pdf config to khoj content-type config
-                // Set pdf config to index pdf files in configured obsidian vault
-                data["content-type"]["pdf"] = {
-                    "input-filter": [pdfInVault],
-                    "input-files": null,
-                    "embeddings-file": `${khojDefaultPdfIndexDirectory}/${indexName}.pt`,
-                    "compressed-jsonl": `${khojDefaultPdfIndexDirectory}/${indexName}.jsonl.gz`,
+                const hasPdfFiles = app.vault.getFiles().some(file => file.extension === 'pdf');
+
+                if (hasPdfFiles) {
+                    data["content-type"]["pdf"] = {
+                        "input-filter": [pdfInVault],
+                        "input-files": null,
+                        "embeddings-file": `${khojDefaultPdfIndexDirectory}/${indexName}.pt`,
+                        "compressed-jsonl": `${khojDefaultPdfIndexDirectory}/${indexName}.jsonl.gz`,
+                    }
+                } else {
+                    data["content-type"]["pdf"] = null;
                 }
             }
             // Else if khoj is not configured to index pdf files in configured obsidian vault
             else if (khoj_already_configured &&
-                (data["content-type"]["pdf"]["input-filter"].length != 1 ||
-                data["content-type"]["pdf"]["input-filter"][0] !== pdfInVault)) {
-                // Update pdf config in khoj content-type config
-                // Set pdf config to only index pdf files in configured obsidian vault
-                let khojPdfIndexDirectory = getIndexDirectoryFromBackendConfig(data["content-type"]["pdf"]["embeddings-file"]);
-                data["content-type"]["pdf"] = {
-                    "input-filter": [pdfInVault],
-                    "input-files": null,
-                    "embeddings-file": `${khojPdfIndexDirectory}/${indexName}.pt`,
-                    "compressed-jsonl": `${khojPdfIndexDirectory}/${indexName}.jsonl.gz`,
+                (
+                    data["content-type"]["pdf"]["input-files"] != null ||
+                    data["content-type"]["pdf"]["input-filter"] == null ||
+                    data["content-type"]["pdf"]["input-filter"].length != 1 ||
+                    data["content-type"]["pdf"]["input-filter"][0] !== pdfInVault)) {
+
+                let hasPdfFiles = app.vault.getFiles().some(file => file.extension === 'pdf');
+
+                if (hasPdfFiles) {
+                    // Update pdf config in khoj content-type config
+                    // Set pdf config to only index pdf files in configured obsidian vault
+                    let khojPdfIndexDirectory = getIndexDirectoryFromBackendConfig(data["content-type"]["pdf"]["embeddings-file"]);
+                    data["content-type"]["pdf"] = {
+                        "input-filter": [pdfInVault],
+                        "input-files": null,
+                        "embeddings-file": `${khojPdfIndexDirectory}/${indexName}.pt`,
+                        "compressed-jsonl": `${khojPdfIndexDirectory}/${indexName}.jsonl.gz`,
+                    }
+                } else {
+                    data["content-type"]["pdf"] = null;
                 }
             }