Handle parallel site updates

### Information about bug

Parallel site updates can fail occasionally due to movement of sites while reading site_config.json
Needs to be handled in agent

### Steps to Reproduce

https://support.frappe.io/helpdesk/tickets/68459

### Relevant log output / Stack trace / Full Error Message.

```shell

```

Start in the agent code that reads site_config.json and use the support ticket linked in the issue to understand the parallel-update failure. Reproduce site movement during a concurrent update, then verify that parallel site updates complete without an intermittent read failure.

Written by the indexing model from the issue text.