I used to think there were two types of emotions.

One kind are emotions caused by purely biological factors. For example some types of biochemical disorders can cause anxiety or depression.  My view is that in gnereal meditation cannot do a lot to help with these types emotion. It might help you cope or reduce your aversion to the emotion, but in most cases it won't make the underling emotion go away.

A second type of emotion is caused by a thought. For example you remember something from your past and you feel anger. This type of emotion can be very effecively dealt with through meditation. When you notice the thought arise and see the emotion follow it and then see the thought fade away and the emotion fade too you  see the emotion is impermanent and is an illuison and with practice you can learn just to relax and let go of the thought and the emotion fades.

Recently I recognized he existence of a thrid type of emotion that doesn't fit into either category. It is an emotion that requires cognition but you don't notice the thought that causes it. Something happens and then you experience an emotion. It must require some cognition because you have to be aware of the event that caused it but you don't notice a thought process leading to the emotions.  For example, someone is talking loudly on their cell phone in a public place that should be pleasant and tranquil and you feel annoyance. You might think, "that person is a so and so", but that is not what causes the emotion, the emotion comes first and then the thought. It's like the cognitive process that produces the emotion is either unconscious or coming from a differnt part of the brain than the second type of emotions I defined above. (Maybe a  lot of these types of emotions are be fuounded in a belief in the self? The self is so implicit in most of our thinking and we don't notice it.)

Some of the greatest suffering comes from this third type of emotion and I never even understood it as a distinct phenomenon so I am wondering about how to deal with them through meditation. Maybe something similar to the the way to deal with the second class is right: Notice the feeling arise, understand it arises in response to an event therefor it is impermanent, an illusion and then try to let go of the emotion by relaxing?  But part of why these can be hard to let go of is that they are a continuous process. If it happened for a second you could let go of it, but if it continues for ten minutes you are overwhelmed. 

I am wondering if anyone has any thoughts about this and what is an effective way to let go of these types of emotions.

There is a fourth phenomenon that I think belongs in this discussion too. Physical discomfort. Pain, an itch, hunger. We want to scratch an itch or eat when hungry. Is there a way learn to let go of that desire through meditation? Wouldn't the same process help reduce suffering from pain?

What I have heard from people who have been on retreats where you have to sit completely sitll is that if you endure it, eventually something changes and you stop suffering over it. Has anyone here had this experience? Does it generalize to all types of physical discomfort?

A helpful way to look at this is through the lens of dependent co-arising. Contact through one of six senses leads to feeling (liking or disliking) which leads to clinging (wanting or aversion) which leads to craving (desire for it to happen again or worrying that it will happen again). It's really great practice to watch this process happen in realtime and avoid getting to the third step of clinging. Contact and feeling often arise at the same time but with diligent mindfulness, the thought/emotion can be dropped there so that one can return to being a happy human!    

Letting the emotion flow while relaxing (surrendering to it, not resisting) seems to be the right approach.

It is not relaxing with the expectation the relaxation will make the feeling go away - like relaxing a tension. It is like relaxing as in not resisting.

Like letting it rise an pass away naturally is the fastest way to get over it and relaxing will prevent any suppression or continuing resentment..

https://www.accesstoinsight.org/lib/authors/thanissaro/onetool.html

I think there is a very good reason for including samatha, and jhana in any type of practice. Stress hormones can cause mental fixation on the source of stress. For example if  you have a disagreement with someone at work, the argument might keep playing over and over in your head. Your biology is keeping you attached.

This fixation might help you to survive if the stress is being caused by a wolf stalking you in the woods, but it might not be that helpful if the stress is caused by someone talking loudly on their cell phone in a public place.

What if there was a type of meditation that reduced levels of stress hormones and helped you to let go of the argument instead of being fixated on it?  Smatha, jhana, will help you to relax and reduce levels of stress hormones and help you to let go.

I think these three types are all the same with different levels of awareness. Any emotion is going to have biological factors as well as thoughts that lead up to it, and the two influence each other. Low blood sugar, depression, illness, and so forth can all make negative thoughts more likely and negative thoughts in turn can cause physical changes.

And there's always going to be some degree of thought trail leading up to it that you aren't aware of - it just depends on how much attention you're paying to your thoughts at the time.