--- a/htaccess.module
+++ b/htaccess.module
@@ -119,15 +119,15 @@
 function htaccess_generate_default(){
   $htaccess_template = file_get_contents(HTACCESS_TEMPLATE_PATH);

-  $with_www_default = "#RewriteCond %{HTTP_HOST} .\n";
-  $with_www_default .= "#RewriteCond %{HTTP_HOST} !^www\. [NC]\n";
-  $with_www_default .= "#RewriteRule ^ http%{ENV:protossl}://www.%{HTTP_HOST}%{REQUEST_URI} [L,R=301]\n";
+  $with_www_default = "#RewriteCond %{HTTP_HOST} ." . PHP_EOL;
+  $with_www_default .= "#RewriteCond %{HTTP_HOST} !^www\. [NC]" . PHP_EOL;
+  $with_www_default .= "#RewriteRule ^ http%{ENV:protossl}://www.%{HTTP_HOST}%{REQUEST_URI} [L,R=301]" . PHP_EOL;

-  $without_www_default = "#RewriteCond %{HTTP_HOST} ^www\.(.+)$ [NC]\n";
-  $without_www_default .= "#RewriteRule ^ http%{ENV:protossl}://%1%{REQUEST_URI} [L,R=301]\n";
+  $without_www_default = "#RewriteCond %{HTTP_HOST} ^www\.(.+)$ [NC]" . PHP_EOL;
+  $without_www_default .= "#RewriteRule ^ http%{ENV:protossl}://%1%{REQUEST_URI} [L,R=301]" . PHP_EOL;

-  $search = array("%%%rules_before%%%", "%%%prevent_txt%%%", "%%%symbolic_links%%%", "%%%ssl_force_redirect%%%", "%%%with_www%%%", "%%%without_www%%%", "%%%boost_rules%%%");
-  $replace = array("", "", "+FollowSymLinks", "", $with_www_default, $without_www_default, "");
+  $search = array("\xEF\xBB\xBF", "\r\n", "%%%rules_before%%%", "%%%prevent_txt%%%", "%%%symbolic_links%%%", "%%%ssl_force_redirect%%%", "%%%with_www%%%", "%%%without_www%%%", "%%%boost_rules%%%");
+  $replace = array('', PHP_EOL, "", "", "+FollowSymLinks", "", $with_www_default, $without_www_default, "");

   $htaccess_update = str_replace($search, $replace, $htaccess_template);

@@ -153,19 +153,15 @@
     ->fetchAssoc();

     if($htaccess_deployed){
-
       $htaccess_deployed = $htaccess_deployed['htaccess'];

-        // Compare the two results
-        if($htaccess_current === $htaccess_deployed){
-
-          variable_del('htaccess_altered');
-
-        }
-        else{
-
-          drupal_set_message(t('The htaccess seems to be altered.'), 'warning');
-          variable_set('htaccess_altered', true);
+      // Compare the two results
+      if($htaccess_current === $htaccess_deployed){
+        variable_del('htaccess_altered');
+      }
+      else{
+        watchdog('htaccess', t('The htaccess seems to be altered.'), NULL, WATCHDOG_ERROR);
+        variable_set('htaccess_altered', true);
       }
     }
   }

--- a/htaccess.admin.inc
+++ b/htaccess.admin.inc
@@ -192,6 +192,14 @@
   $htaccess_count = count($htaccess);

   for ($i=0; $i<$htaccess_count; $i++) {
+    // Check that the profile is not in use
+    $htaccess_check = db_select('htaccess', 'h')
+      ->fields('h')
+      ->condition('deployed', 1, '=')
+      ->condition('id', array(':id' => $htaccess[$i]->id),'IN')
+      ->execute()
+      ->fetchAssoc();
+
     $form['htaccess_settings_version']['row_' . $i] = array(
       '#prefix' => '<tr class="'.($i % 2 ? "odd" : "even").'">',
       '#suffix' => '</tr>',
@@ -199,7 +207,7 @@
     $form['htaccess_settings_version']['row_' . $i]['htaccess_settings_version_number'] = array(
       '#prefix' => '<td>',
       '#suffix' => '</td>',
-      '#markup' => $htaccess[$i]->id,
+      '#markup' => $htaccess[$i]->id . ($htaccess_check? '*' : ''),
     );
     $form['htaccess_settings_version']['row_' . $i]['htaccess_settings_version_created'] = array(
       '#prefix' => '<td>',
@@ -217,7 +225,9 @@
       '#markup' => $htaccess[$i]->description,
     );
     $form['htaccess_settings_version']['row_' . $i]['htaccess_settings_version_operation'] = array(
-      '#markup' => l(t('View'), 'admin/config/system/htaccess/deployment/view/'.$htaccess[$i]->id.'') . ' ' . l(t('Deploy'), 'admin/config/system/htaccess/deployment/deploy/'.$htaccess[$i]->id.'') . ' ' . l(t('Download'), 'admin/config/system/htaccess/deployment/download/'.$htaccess[$i]->id.'') . ' ' . l(t('Delete'), 'admin/config/system/htaccess/deployment/delete/'.$htaccess[$i]->id.''),
+      '#markup' => l(t('View'), 'admin/config/system/htaccess/deployment/view/'.$htaccess[$i]->id.'') . ' ' . l(t('Deploy'), 'admin/config/system/htaccess/deployment/deploy/'.$htaccess[$i]->id.'') . ' ' . l(t('Download'), 'admin/config/system/htaccess/deployment/download/'.$htaccess[$i]->id.'') . ' ' .
+      ($htaccess_check? '' :
+      l(t('Delete'), 'admin/config/system/htaccess/deployment/delete/'.$htaccess[$i]->id.'')),
       '#prefix' => '<td>',
       '#suffix' => '</td>',
     );
@@ -318,12 +328,6 @@

   $htaccess_content = $htaccess_get['htaccess'];

-  // Remove utf8-BOM
-  $htaccess_content = str_replace("\xEF\xBB\xBF",'', $htaccess_content);
-
-  // Standardize the EOL.
-  $htaccess_content = str_replace("\r\n", PHP_EOL, $htaccess_content);
-
   // Try to write to the .htaccess file
   if (file_put_contents($htaccess_path, $htaccess_content)) {
     drupal_chmod($htaccess_path, 0644);
@@ -375,9 +379,6 @@
     ->fetchAssoc();

   $htaccess_content = $htaccess_get['htaccess'];
-
-  // Remove utf8-BOM
-  $htaccess_content = str_replace("\xEF\xBB\xBF",'', $htaccess_content);

   $file_name = $htaccess_get['name'].'.htaccess';

@@ -511,8 +512,9 @@
     $prevent_txt_rules .= '</FilesMatch>' . PHP_EOL;
   }

-  $search = array("%%%rules_before%%%", "%%%prevent_txt%%%", "%%%symbolic_links%%%", "%%%ssl_force_redirect%%%", "%%%with_www%%%", "%%%without_www%%%", "%%%boost_rules%%%");
-  $replace = array($rules_before_config, $prevent_txt_rules, $symbolic_links_config, $ssl_force_redirect, $with_www_config, $without_www_config, $boot_rules);
+  // Include removal of any BOM, and standardise EOL.
+  $search = array("\xEF\xBB\xBF", "\r\n", "%%%rules_before%%%", "%%%prevent_txt%%%", "%%%symbolic_links%%%", "%%%ssl_force_redirect%%%", "%%%with_www%%%", "%%%without_www%%%", "%%%boost_rules%%%");
+  $replace = array('', PHP_EOL, $rules_before_config, $prevent_txt_rules, $symbolic_links_config, $ssl_force_redirect, $with_www_config, $without_www_config, $boot_rules);

   $htaccess = str_replace($search, $replace, $htaccess_template);