Thank you for your reply.
I experience a transmutation of the uncomfortable emotion into a positive one. Later I feel negative emotions in the area, say the solar plexus, more strongly - probably because I become more sensitive or a deeper layer come forth. This all makes sense to me, and I accept that as a part of the process.
The reason I'm asking though is that, as I understand it, trauma is stored in the brain stem and by letting go of the emotions related to the trauma, the trauma gets healed permanently. However, I fear that controlling my states by holding a positive thought/intention will not permanently heal the trauma. Instead there will always be the risk that it shows up if I'm not diligent with my intention. Whereas a healing of the trauma will cause it to never arise again.
Then I was thinking that maybe the trauma does get healed somehow, but that I just don't understand how it occurs. That is why I'm asking you.
Does that make sense?