Do I understand you correct that you have now received an email telling you which geocaches you have lost the favorite points on? Otherwise I will gladly try to investigate it for you.
But as mentioned before, there is a big risk that it just takes some extra time. Project-GC does not detect any changes instantly. Most changes takes about 24 hours, but some takes more time, like for example, editing of logs or removal of FP. The workflow is quite hard to explain and can almost be seen as random. But the more active the geocache is, the faster it goes.
