I don’t know why, but the study interval for my entire deck has been reset. All the cards were still in “Learning” mode, so they now appear as if I’ve never seen them before.
What I did was update Anki from 25.07 to 25.09, and I moved the cards into sub-decks.
I don’t know what to do; this is now costing me a lot of time.
Did you change the number or length of learning steps as well? Or move them between Options presets with different steps?
Yes, when I moved the cards, the default setting was different, so I changed it to my own custom setting. Was that the mistake?
Changing steps while you have cards in Learn/Relearn can cause skipped or repeated steps – which is what I think you’re seeing here.
If you can restore a backup from before you did that (without losing too much) – Restoring an Automatic Backup (Recovering from Data Loss) - Anki FAQs – you might be able to avoid this happening in the first place. You’ll lose any review history and edits you’ve done since then. If you can’t afford to lose that, there are other ways to approach this, but they are less “clean.”
Alright, thanks for your support, but I think it’s too late for a backup 
Okay, let’s go the other route.
First – you’re using multi-day learning steps. Is that because you’re still using the default SM-2 algorithm? If you haven’t enabled FSRS, I’d recommend doing that now.
[Before you optimize your parameters, if you have a lot of subdecks, you should make sure they are assigned to the Options presets you think they are, or FSRS won’t see them.]
You’ll notice that includes setting your cards to have only one short (5m-30m) learning step and relearning step. That’s obviously a big change from what you’re used to, but FSRS will do a better job of scheduling your cards for intervals based on their review history, than the strict set of learning steps you’re using now to treat every card the same. If you decide to keep multiple steps, make sure it’s only the short ones, so you can graduate all of your cards from Learn/Relearn every day.
Then, as far as dealing with these cards – how many cards do you have in Learn/Relearn right now? They should graduate to Review (and FSRS will schedule their intervals) the next time you study them and grade them Good.
If it’s not too many cards, and you want to consider them individually (and especially if you decide to keep multiple steps), you could look at each of them and decide whether they –
Cards > Set Due Date on those to convert them to Review cards – Browsing - Anki Manual . Depending on how many cards they are, you can sprinkle them across a few days [0-3], or set them all to today [0].