A couple folks have reported this in the the NetBeans forums and issue tracker. I haven't been able to reproduce it... but am still looking for more info...
NetBeans does allow you to undeploy an application or module. That capability is exposed in the Services Tab when the server/domain is running (which would explain why you are having trouble finding it...
I would discourage you from renaming directories and file in the "internals" of the server. I have only heard of a couple folks successfully debugging/working around an issue using such a tactic. Most of the rest ended up with servers so confused that nobody was able to determine the root cause of the issue that triggered the "maybe if I rename this..." response.
vbk
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