3.4.5 v membership plugin blogs disappeared question

I updated to the latest v of membership plugin 3.4.5 yesterday and some of my subsites have disappeared. They don't show when I use a shortcode to display sites and I also cannot access the sub sites by entering their urls. Eg http://mysite.com/subsite just takes me back to http://mysite.com.

The "path Update siteurl and home as well." section is unchecked in network> sites for the sites that have disappeared. For the blogs that are still there the "path Update siteurl and home as well." section is still selected.

The url groups have also disappeared with the update.

Any ideas on what can cause / how to fix this?

I just reverted to yesterday's backup with v 3.4.2 and everything is running well again. The only other changes that I made yesterday were to install site categories plugin and add some fields in Adminimize plugin. In this thread I think we ruled out that site categories didn't cause the problem. https://premium.wpmudev.org/forums/topic/will-site-categories-conflict-with-marketpress-categories. Could the issue be with membership v 3.4.5?