Pre-post: I have skimmed the two most recent pages of the Cartographer forum (to get back before the 2.2 patch) for this issue and turned up nothing similar, so here we go in the hopes that I'm not completely blind.
Problem: When I hit a node that's already on my map, it seems like the built-in cleanup/re-mark function isn't going all the way. It simply erases the old node from the map. Spamming clicking the node does not help. If there is no node on the map, for instance if I delete the note for the node before I mine it, it shows up like it should. If I go back and mine the same after doing so, it disappears again. Once this happens, the note will never show up for this node again, no matter how many times I've mined it afterwards.
To be sure it was only fel iron, adamantite and khorium, I went back and mined a few old world nodes, copper, tin, mithril and thorium. All worked perfectly fine. The one thing I did note here though is that all of these node marks were spot on the node, and perhaps didn't need to be removed/re-marked by Cartographer? _But_ even when the fel iron I've been getting lately has been spot on the node, it still erases it without replacing it.
Previous to the patch, I was running Cartographer and Gatherer, and other than some issues with look 'n feel and Gatherer's world map nodes, they coexisted peacefully. To be sure it wasn't some hooking issue (or sure in my mind) I removed Gatherer and its database entirely from the addons and WTF folders. Issue persisted. I removed Cartographer completely then and put Gatherer back in. Same issue, except that Gatherer doesn't do node moving. It would not mark any Outlands veins as gathered if they were already received from another guild member, nor would it mark completely new gathers.
Going back a bit, on the day of the 2.2 patch, I completely rebuilt my UI, as in I wiped my addons folder and my WTF folder completely and started over. Everything I have should be the most up-to-date versions, and I run WUA probably twice a day or more (pesky Omen bugs!).
I also use Cartographer_Herbalism, but it does not seem to share this seemingly Outlands-related bug.
Any suggestions, fixes, beratings, etc are welcome.