@Cherny, Igor Thanks for clarification! I discussed this internally and came out- this might be a transient error and the chunks may be getting deleted in the next indexer run.
We recommend keeping an indexer on a schedule for any transient errors to be fixed in the next run: Indexer errors and warnings - Azure AI Search | Microsoft Learn.
If you have the indexer running on a schedule and the file is not deleted in the next run(s), suggest you to create support ticket for deeper understanding if this is something we need to fix from the product side.
Having said that reached you privately.
Hope this helps.