I hate to be the bearer of bad news here, but if you accidentally deleted repository metadata, there is no way to get it back of which I am aware.
The metadata that was deleted (not knowing everything missing, but guessing) contained the information concerning which indices contained which segments, and which snapshots contained which indices (and their associated segments). If that data is gone, there is no way to re-create it. Even if the snapshotted data (the index segments themselves) is intact, it is useless without the metadata that allows Elasticsearch to reconstruct them into a viable index.
Now, based on what I'm seeing in this message:
You appear to have deleted some of your segment data. The snapshot metadata may actually be intact, but files it requires to be able to reconstruct certain indices are gone. You can still restore from this repository, but it will be missing some data (how much depends on what, exactly, was deleted). You only need to set partial: true during a restore for this to work. Unfortunately, you will not likely be able to snapshot to this repository in this state. It won't let you because it's not healthy.
Potential solutions include restoring what data you have to a temporary cluster and re-snapshotting it to a re-made repository.