The server I help run has been plagued with this problem for quite some time.
Thaumcraft Nodes just... up and die. Disappear. I thought it was because they were being drained of vis, because I drained a node and left it that way overnight and it disappeared (the first one, actually) but... nobody was doing anything that intensive near the spawn community buildings, and the nodes near there died.
Pretty much all the dying nodes are in areas loaded by chunkloaders and/or heavy use areas (spawn community area, my apiaries in twilight forest, a few mystcraft ages). Heavy use as in folks are there almost always, not so much heavy Thaumcraft usage. (We've got one or two Thaumcraft folks on the server, the rest are just learning).
One of the server members (that I have a hard time believing) says it's a tick error in Thaumcraft, but... yeah...