Is the server unmodded or, if you did apply mods, do you have multiple mods?
I ran a server modded with Khaine's ever-so-lovely Darkness Falls overhaul mod for my friends and I to enjoy a persistent world together. Everything ran A-Ok for several months. While DF didn't cause us to wipe the server and start over, a glitch with another mod did.
For the lulz, we tried out Boid's Infinite Horde mod, in addition to DF. We did understand that the two might not work well together. For a time, however, everything seemed be stable. Even so, we ended up removing BIH after a few Blood Moons because we could not always be online at the same time for horde night. I was reasonably certain that I had deleted the BIH mod from /7 Day To Die/Mods, but the following Blood Moon threw an un-ending stream of zeds at us as if BIH was installed. The issue persisted even after we created an RWG map.
I should have contacted Boidster or asked for advice on here or Discord; however, I was too busy with work to do so at the time and just reset the server to its default. After the reinstall and subsequent re-addition of DF, our new RWG map ran properly, with the Blood Moons and freaky demons occurring as we had come to expect.
I hope that you do not end up having to resort to a similar solution, no matter your situation.