So I have an interesting situation. Basically, team beat crota few min before 48 hours was done and saw we didn't get the triumph to pop up. Some people said maybe to wait and see if it pops up along with the chest (since during VoTD day 1 there were times were we needed to wait a few min after beating an encounter before the chest with loot spawned cause of the server issues so that's were our train of thought went) and so we waited until like 5-6 min after reset before going to orbit.
TLDR: beat crota challenge along with other challenge encounters before 48 hours was done, went to orbit 6 min after 48 hours was done. Wondering if it will count us killing crota before the 48 hours and we will be given the emblem or because we didn't go to orbit until 6 min after if the clear of challenge won't count being completed within the 48 hours and we won't get our emblems.
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As long as crota was killed on challenge and the chest + timer both appeared prior to daily reset you should be fine for getting the crota triumph (and emblem if you did the other challenges)