Helped me to get rid of "unix-all-logs" eventtypes:
1) move "unix" app from folder etc/apps
2) restart splunk
3) copy "unix" app back to etc/apps folder
4) restart splunk
In the case of the *nix app on my instance, I chose overwrite with 4.2.0 from the splunk -> manager -> apps window.
So long as they follow the standard that is outlined below, the method should be the same, as far as I understand it. 4.1 did not behave in this manner.
http://www.splunk.com/base/Documentation/latest/Developer/Migrate41x
what about apps i've downloaded from splunkbase that weren't originally included with Splunk?