Hmmm, for mine, it worked as soon as I had added it to the index - it then took a few days for the videos themselves to show up in the index. One thing I could imagine happening might be, that maybe videos already on the instance before it was added on the index will take even longer? In that case, maybe removing and re-adding them might work? But that's a wild guess.
Another thing that may have happened - if adding the instance recently definitely isn't the problem - maybe it got blacklisted from sepiasearch somehow? But if that were the case, I don't think they'd do it in a "shadowban" way, and the instance would just be removed from the index - unless I am misremembering their moderation policies.
Whatever is causing it, here's hoping you'll have a solution soon, and good luck solving the issue.