I have a similar issue: yesterday I had 8 hours to get garnets from Mt Despair and I was able to retrieve 4 garnets. But every time I crafted the trinket it simply did not update. I had no ability to update the Goddess Tree. Consequently I have to go to Mt Despair again without the benefit of the potion to look for another garnet - a sync error that occurs four times without a result sounds like a coding error not a sync error.