A friend from Syria once told me that in their country flashing warning lights means "f* you", and when he saw it for the first time when going abroad, he was really angry when someone thanked him. Like "I've just let him merge and that is how he acts to me?!"
But I personally haven't heard of any other cases when this isn't considered a thank you gesture
In Israel the most common meaning is "Get off my lane, RIGHT NOW!", so I wouldn't be surprised if it's not just Syria but a big chunk of the Middle East that follows that rule.
It could also be used to call another driver's attention (e.g. if you have a broken taillight and did not notice), or to warn against a police trap (in the pre-Waze era) and maybe a few other things, but it never means "thank you".
Car coming the other way flashes and it means hazard ahead.
If it's at night and your DRLs are the only thing on it means "turn on your lights moron"
At an intersection it usually means "go" to whichever party should be yielding to the flashing party.
Of course if you're in the left land and flash your brights at someone who's clogging up the left lane there's a good chance they won't understand it because if they could understand the context they wouldn't be clogging up the left lane in the first place.
I'm surprised at the thank you gesture. The intended use of warning lights is to... warn people, right? I've always understood them to mean "something weird has happened, and so I may do something unpredictable." I can't see how that could have morphed to "thank you."
Pretty sure the intended use is when stationary, to warn that you have broken down and are positioned badly.
At least, that used to be the only time it was legal to use them here (Sweden). They recently added a rule that it’s legal to use warning lights while being towed, too. Either way, it’s certainly a traffic offense to use them while driving.
But I personally haven't heard of any other cases when this isn't considered a thank you gesture