Hello,
regarding your questions:
- One way is to use custom properties as much as possible and define flat groups using these custom properties. You should be able to assign custom properties to most of objects and they can be pretty powerful tool for limitations management.
- Are those child groups flat or are they also contain other groups?
- There were some changes related to limitations so some of them might affect your case. If it worked before and you haven't changed the groups or haven't added bigger amount of new items then it would be good to open a support ticket. It may really be some issue.