Whenever another mod is tempering with the region files directly, an anchor/vault may be removed.
In this case, the files on the server still indicate the presence of an anchor/team.

Could it be an idea to periodically check for the presence of anchor/vault to avoid the persistence of chunks/teams when the corresponding block is not there anymore?

I will look into this. However (if I recall correctly), when you try to place an anchor in a chunk where an anchor already exists according to the files, the mod will check to make sure the anchor is actually there. If it isn't there, it will correct the issue.

I did not try that.
I was actually wondering more if this would not be an issue for payments of chunkloading.
In other words, a player would have a hard time stopping the chunk loading if the anchor is lost.
He may have to place alot of anchors before finding the chunk that is "bugged" and thus correcting the issue.