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Be careful about which preference settings relate to the functionality in question.
1. Tools > Preferences > Environment > Local History > Enable relates to a worksheet's History tab when you File > Open
2. Tools > Preferences > Database > Worksheet > SQL History Limit relates to View > SQL History pane.
You do not say how you backed up and restored your settings during all your experimentation, but let's assume whatever you did was valid. Whenever some UI component mysteriously disappears, one thing I always check (usually just delete) is the windowinglayout.xml in system3.2.20.09.87\o.ide.184.108.40.206.37.59.48 of my user settings.
For example, I can use the SQL History pane's tab context menu to Float it, then adjust it's size by dragging it's edges down to a grey square a few pixels wide/high. Close SQL Developer, reopen, View > SQL History. Darn! Where did it go?
Hope this helps,