Commenting and upvoting for visibility: I can confirm that this is a fixable issue, as I posted a similar issue and my team's run was added back into the API. One of my teammates had been following it closely and noticed that total clears on the raid.report leaderboard went from 675 to 676 when our team's clear had been updated. If Bungie could fix this for all teams impacted by this, that'd be awesome!