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1. Register MySQL server. 2. Rightclick "Databases" node and choose "New Connection". 3. Choose "MySQL" in "Name" drop down list, enter values for "Host", "Port", "User Name" and "Password" fields, then click "Direct URL Entry" radiobutton and click "OK". 4. Expand added connection's node. All databases will be shown. 5. Expand MySQL server's node, rightclick some DB and choose "Delete". Result: DB is deleted and it's node removed under MySQL server's node, but connection node still contains it.
Reassigned to new owner.
NB6.7 was released already - http://www.netbeans.org/community/releases/67/ Postpone fixing this issue on the next release.
No plan to fix it, a user has to understand all consequences if delete a database. Reopen it if I'm wrong.