This was my thought also. The first sentences of the RCA screamed “race condition” without even having to mention the phrase.

The two DNS components comprise a monolith: neither is useful without the other and there is one arrow on the design coupling them together.

If they were a single component then none of this would have happened.

Also, version checks? Really?

Why not compare the current state against the desired state and take the necessary actions to bring them inline?

Last but not least, deleting old config files so aggressively is a “penny wise pound foolish” design. I would keep these forever or at least a month! Certainly much, much longer than any possible time taken through the sequence of provisioning steps.