Try 2: Completely redo how themes are stored on disk and processed at install time.

chrome/browser/extensions/theme_installed_infobar_delegate.cc

 // Copyright (c) 2009 The Chromium Authors. All rights reserved.
 // Use of this source code is governed by a BSD-style license that can be
 // found in the LICENSE file.
 
 #include "chrome/browser/extensions/theme_installed_infobar_delegate.h"
 
 #include "app/l10n_util.h"
 #include "app/resource_bundle.h"
 #include "base/string_util.h"
 #include "chrome/browser/extensions/extensions_service.h"
 #include "chrome/browser/profile.h"
 #include "chrome/browser/tab_contents/tab_contents.h"
 #include "chrome/common/extensions/extension.h"
 #include "grit/generated_resources.h"
 #include "grit/theme_resources.h"
 
 ThemeInstalledInfoBarDelegate::ThemeInstalledInfoBarDelegate(
     TabContents* tab_contents, const Extension* new_theme,
     const std::string& previous_theme_id)
          : ConfirmInfoBarDelegate(tab_contents),
            was_canceled_(false),
            profile_(tab_contents->profile()),
            name_(new_theme->name()),
            new_theme_id_(new_theme->id()),
            previous_theme_id_(previous_theme_id) {
 }
 
 void ThemeInstalledInfoBarDelegate::InfoBarClosed() {
   ExtensionsService* service = profile_->GetExtensionsService();
-  if (service) {
+  // Only delete the theme if we've installed a new theme and not the same
+  // theme on top of the current one.
+  if (service && previous_theme_id_ != new_theme_id_) {
     std::string uninstall_id;
     if (was_canceled_)
       uninstall_id = new_theme_id_;
     else if (!previous_theme_id_.empty())
       uninstall_id = previous_theme_id_;
     // It's possible that the theme was already uninstalled by someone so make
     // sure it exists.
     if (!uninstall_id.empty() && service->GetExtensionById(uninstall_id, true))
       service->UninstallExtension(uninstall_id, false);
   }
@@ skipping 44 matching lines @@
       if (previous_theme) {
         profile_->SetTheme(previous_theme);
         return true;
       }
     }
   }
 
   profile_->ClearTheme();
   return true;
 }