ouch - hate to say this but first time I've heard about this issue ;(
And yes, patching should not end up with this broken situation.
Could you please open a bug on Tools (JBoss Tools) - JBoss Issue Tracker with the steps you used ? ( including which exact runtime and which exact zip ?)
I'll ping my server contacts to figure out if this is something they have seen.
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I just got confirmation this actually is an expected sideeffect - but that breaks alot of things thus I would really appreciate if you would still open an issue and
I'll hunt down where this went wrong.