Updated to 3.5 end same problem here (multisite installation). Al translated pages generate a 404. If I go to settings of url moodifications, change nothing but just press save again, everything works again. If I then go to settings > permalinks and save the permalinks, the issue occurs again resulting in a 404 for all translated pages. Got the plugin running on the site for 4 years, never had this problem. Also occurs when using a default twentytwentythree theme.
Is this known and is there a fix comming?
PS. The site is very basic, no custom post types or anything.