diff --git a/lib/github-manager.php b/lib/github-manager.php
index 6d1781b..18eb694 100644
--- a/lib/github-manager.php
+++ b/lib/github-manager.php
@@ -52,6 +52,10 @@ if (!$demoMode && isset($_SESSION['loggedIn']) && $_SESSION['loggedIn'] && isset
 				$fh = fopen($settingsFile, 'w');
 				fwrite($fh, $settingsContents);
 				fclose($fh);
+
+				// Clear any FTP session we may have
+				$_SESSION['ftpSiteRef'] = false;
+
 				// Hide this popup and reload file manager
 				echo "<script>top.ICEcoder.showHide('hide',top.document.getElementById('blackMask'));top.ICEcoder.refreshFileManager();</script>";
 			} else {
diff --git a/lib/go-localhost-root.php b/lib/go-localhost-root.php
index 26af7a5..82d98aa 100644
--- a/lib/go-localhost-root.php
+++ b/lib/go-localhost-root.php
@@ -22,6 +22,10 @@ if (!$demoMode && isset($_SESSION['loggedIn']) && $_SESSION['loggedIn']) {
 		$fh = fopen($settingsFile, 'w');
 		fwrite($fh, $settingsContents);
 		fclose($fh);
+
+		// Clear any FTP session we may have
+		$_SESSION['ftpSiteRef'] = false;
+
 		// Now we've reset the root path to localhost root, refresh the file manager to show it
 		echo "<script>top.ICEcoder.refreshFileManager();</script>";
 	} else {