When a scheduled server backup starts while a SafeUpdates run is still processing plugins, the update queue can stop before completing the full list. In that situation, only part of the selected plugins are applied and the remaining ones stay pending.
The current behavior is difficult to detect because:

The update log only shows the plugins that were processed.
The notification email does not indicate that the run was interrupted.
There is no warning when a backup schedule overlaps with the SafeUpdates window.

Suggested improvements:

Add a warning in the Auto Updates scheduling UI when a server backup time overlaps with the SafeUpdates window.
Include a clear message in the SafeUpdates email or update log when a run is interrupted and not fully completed.

This would make it much easier to understand when an automation did not finish as expected.