This is the second time this has happened. If I recall, the last time it happened I ended up having to reinstall Komplete. 
 
I ran the service center and clicked "install" on all the updates. The net result is that many of my NI effects have simply disappeared. In fact I managed to witness one of them disappear from the plugin folder as it was installing the update. Passive EQ. It was there in the folder, clicked install and watched it disappear into thin air. 

When I ran the service center again (after a reboot), there is nothing available in the updates. It's as if NI has just wiped out all record that I own the plugins. YAWN I cannot be bothered with this nonsense.....

Probably a stupid question, but just trying to help:
Did you manually move any of the stuff since it was last installed?
The NI service Center remembers where it installs everything (or at least it is supposed to).
If you manually move things after an installation unpredictable things could happen.

Yeah I thought that maybe it had something to do with that. But I haven't moved anything since I last ran the Service Center, and those updates went fine. 
 
The other curious thing is the existing dll's disappearing. I presume that an updater deletes the existing file and installs the new one. Well it deleted the existing ones alright - suggesting that it had the correct install location - it just didn't install the new ones. 

I previously had an issue as well, probably due to a Service Center "hiccup" ~
 
After logging in to the NI site, you can manually download & install the updates for the "disappearing" plugins from here:
 
http://www.native-instruments.com/en/support/downloads/updates/
 
The manual install seemed to have "realigned" everything, and all seems to be working OK for me now...

Great thanks for that. It's a pain to have to reinstall all of these plugs but I guess if I have to.....

Well in the end I just reinstalled all VST's from the Komplete hard drive and went through all the updates again. Meh I had nothing important on tonight anyway, figured I might as well spend it watching 12,073 progress bars going from left to right. And those updates are always SO much fun given that you have to click "install" on every...freaking...update. 
 
Oh well, everything seems to be good now. Although I did nearly have a heart attack when a project wouldn't load Kontakt, before I realized that you have to run the standalone first. 

There was a thread on this a few weeks ago. I think it was in software. My experience has never been good when installing from Service Center. They install and then delete the download. I always install from the folder and haven't had it happen since I have been doing that.

BassDaddy
I always install from the folder

^^^ THIS ^^^

 
 
Now we know why NI refers to it as the "So-called Service center" in their instructions.    
 
Glad to hear you got everything back in order, Sharke.
 
 

This morning I had issues with fx plugs missing after updating from Service Center. Would run Service Center again and it was wanting me to dl the same plugs I just updated. Looked in the vst folder and they were gone.
 
Did the dl from Service Center and then manually installed. I noticed during the install that the vst was X'ed out so I un-X'ed it out and it installed where it was supposed to. Works fine now but still don't know what X'ed it out. Perhaps an NI conspiracy just to piss people off... 
 
Still have some issue with Evolve R2 not wanting to update because I did move it to a different drive. I can see the reference to the old drive still in the registry. Made a system backup so now it's time to try and make some reg changes. Hopefully it works, After the IK MP2 marathon yesterday I'm getting tired of installing and troubleshooting software...