Hi Elizabeth,
You are totally right about what happened and I hope you can restore your data properly. Some extra information if you're planning to delete that hierarchy again after the restoration ...
Deleting big hierarchies is a demanding operation due to the nested set updates required in the process and, when the operation timeouts in the browser, the rollback takes even longer, which is what you're seeing after restarting MySQL. AtoM includes a task to delete those hierarchies from the CLI avoiding the time constraints from a web request, knowing the slug of the top-level description, run the following command from the AtoM folder to delete the hierarchy (removing memory limitations too in case the hierarchy is that big):
php -d memory_limit=-1 symfony tools:delete-description <slug>
Additionally, if you're working with big description hierarchies you may want to consider upgrading to a more recent version, we have improved the deletion process in AtoM 2.5.4 to a point where I think you should be able to perform that deletion through the interface too, see the related ticket:
And in AtoM 2.6.x, thanks to the upgrade to MySQL 8, we have changed some important hierarchical queries to use CTE:
Best regards,
Radda.