So there is a Bug related to Deep Freezers and Ownership:
Any time the server restarts, ownership of your Freezers is lost!

It might be the case that this bug is only there, since Deep Freezers weren't added in the initial wipe, but later.

But this is not a big enough issue to wipe again, so we will find out at the next (hopefully regular monthly) server wipe.

Treat Deep Frezers as non protected!

Edit: Its a bug, wiping won't help.

The server crashed and deleted all custom items.
I tried to rollback and it deleted the map.

I'm going to vent a bit, so bear with me, as it also explains some stuff:

While the game is still in early access I am still kind of frustrated that this can happen.

Aside from the server crashing, without logs showing why it crashed, I can't update mods or install new ones after the initial wipe.
It just does not download them even if setting up everything right. (Official Klei forum has threads about it, no solutions from devs. I assume they are aware and working on it.)
So if a mod gets an update I can either disable it, or wipe the server.
You can see that with many mods this can be kind of a problem, especially if an important mod like stormcellars is updated.

So the options are to either run the server the stable way with no mods.
Or to install mods and have the risk of the server either crash or a mod update, resulting in a wipe or disabling of updated mod.

Since the server is a public one, mods like ownership are very important, so going vanilla is not an option.

For this wipe I will add mods that some asked for and delete a few.

Sorry guys, I know it sucks that all the work is lost, the bases were really amazing.

The server is running for a month in realtime and over 1500 ingame days.
As such we are going to start a new map.
Full Changelogs will follow, but a few points:

Most mods will stay just a few exchanged.
More mods to make maintance easier.
Wilderness instead of Endless(?) not too sure about it yet.

Wipe will be at the start of July.