Emergency flares:

Helicopters have a second set of flares, but using them massively increases the cooldown of the next set of flares.

For example, flares currently have a cooldown of 30 seconds (give or take). This would be the cooldown of the first set of flares.
However, using the second of set of flares (emergency flares) increases the cooldown of the next set of primary flares by 4 or 5 times.

emergency flares themselves would an even longer cooldown, possibly up to 5 minutes. They could even be single use per helicopter, could be altered based on balancing.

Using emergency would sacrifice downtime at a later date for safety for the present.