If you are in a rainstorm with thunder and lightning - you make the Brachos for them. What happens if the storm ends and then a few hours later (same day) it is raining again. Do you make another Bracha or is it only said once a day?
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As long as it looks overcast, it's once per day.
If it totally completely absolutely clears up bright and shiny, then later thunderstorms, you'd make a new bracha.
Once per day,
Once per cloudy episode
Whichever is more.
(See Shulchan Aruch Orach Chaim 227:2 and Mishna Berura sk 8)
If by "ends", you mean the sky cleared, then yes you make another one. However, just stopping and starting doesn't count.
On an aside, if it's the next day you make a Bracha even if the sky didn't clear.