I would say it is fine to deny the error since it only applies to very few verses. In addition, when it is denied, it is easy to see which verses have been denied. Transparency is important. I knew we had reordered some verses, but I could not remember exactly where it was. By running the verse check and showing denied errors it was easy to see where they were.
We did it 6 places in the Danish Bible. Apart from Isa 38 we reordered in Exo 16 moving 9-11 in between 3 and 4. We reordered 3 places in Prov 31 in order to make the translation acrostic so the verse order is 19, 21, 20, 23, 22, 25, 24, 26. In Job 31 we moved 36-37 down to the end of the chapter. In every place there is a footnote explaining the reasons. This is quite a free translation, and for many projects such reordering might not be acceptable.
Iver+Larsen