I'd agree with vMarkus, it sounds like there are dynamic objects - either VMs, logical switches or some other grouping objects - that are no longer valid. This can happen if the moref identifier changes. For example, a VM may be removed from inventory and added back, which changes it's moref.
Take a look at rules 4 and 5, and if those objects are still around, simply remove and re-add them. That should correct the problem.
Best of luck.