Improvements are made to the applyEdits operation in ArcGIS Pro 3.0 and this issue no longer occurs.
解决办法
Use the Truncate Table tool when connected as an organization admin or service owner with the ArcGIS Online-based services. This method works best in ArcGIS Pro to delete all rows, not just a subset or a selection.
To delete only a subset of the data, make smaller selections records (start with 500), and click Save Edits after each deletion.