てしまう means “ends up doing”, so 降ろされてしまう literally means “end up being lowered.”
We express our feelings of regret by using てしまう, but I don’t think you need to translate it because it’s an expression peculiar to Japanese.
I didn’t know the reason why the national flag ended up being lowered during the night.
I didn’t know the reason why the national was lowered during the night.
I didn’t know the reason why they lowered the national flag during the night.