Do you have a log of the prune run? I’m not completely sure from your description whether prune failed while looking for used blobs or whether this happened while rewriting pack files. However, the repository shouldn’t end up damaged in either of these cases as prune only deletes old pack files after the new ones were written.
You could try to recreate the repository index by running restic rebuild-index. But please create a backup copy of the index folder in your repository to have a way back, in case things get worse.