I agree with you that the chakras contain traumas and dirt in them, and that when you chant a mantra for cleaning or empowering, those traumas and dirt tend to come out.
And that's the thing, you
WILL feel worse off when you meditate, this is why we advise to go with lower reps and only what you can handle.
No affirmation, will help you "bypass" trauma, you
need to feel worse before you feel better, but when you get better, you'll feel so much better. This is just what cleaning does, alongside empowering.
The only thing that helps is Void Meditation to ignore these negative thoughts and feelings as best as you can.
Thoughts are electrical impulses. When we revamp our bioelectricity, we stimulate areas of our minds that have been and are normally dormant. Kundalini can kick up old fears, unpleasant thoughts and all kinds of things that have been buried in our minds.
Void meditation and the ability to banish thoughts at will, is a definite help here, as negative thoughts serve no real purpose and tying into them is a waste of time, unless it is for a specific reason, as one wanting to deal with them. This is just a stage and will pass in time. Ignore any negative thoughts if they surface and they will go away.
https://templeofzeus.org/www.angelfire.com/empire/serpentis666/kundalini-2.html