RPFS index files continually run

Our systems manager has recently left the company and I have been sourced with dealing with this issue. Our repository is currently at 99% capacity. I understand space is only claimed back once the rpfs index files finished deleting. They have been deleting solidly now for at least 5 days. When can I expect them to finish so that space is reclaimed. Learning on the job here so any help would be greatly appreciated.