Depending on the age the first pic looks like the natural woody stem that peppers develop.

Second pic are all the leaves like that or was that a bottom leaf?

third pic looks like damage from transport or some other cause and looks to be healed.

Last pic the purplish color is fairly normal for peppers.

can you post pics of the whole plant or plants?

Also change of environmental factors stresses plants.

Hi habjolokia, regarding the leaves, the larger leaves seemed to be affected the worst, not just the bottom leaves. Smaller leaves had a few black dots on them.

Do you think it's not disease? More like stress, possibly combined with some element of toxins in the system following the cleaning?

I have already cut off all the damaged leaves from the plants to limit any spread if it was a disease.

Your environment seems fairly controlled, so soil born diseases/problems can be ruled out. Have you checked for aphids? They can cause the type of leaf damage you are seeing and can carry diseases to pass onto your plants.

It could be shock and adjustment to the new system to include a possibility of reaction to the cleaning agent. Though it seems that three good flushes should be fine.

How are the top brand new leaves doing?

That leaf damage looks like it's mechanical. Did you spray them recently with something or some type of chemical residue condensed and "rained" from the tunnel ceiling?

Kevin

Hi woohooman, no sprays or sprinklers used. No evidence of any aphids or any other pests in response to previous question.

How does the new growth look?