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Do you have Databases for EE and SE sharing same oradata folder?
Shutdown EE databse and copy the datafile folder for ee into another location.
create the oradata folder again
copy back the ee database datafiles(make sure you have same structure as before)- I did not try it myself ;)
Hope i got you right..
How To Deinstall/Uninstall Oracle Home In 11gR2 [ID 883743.1]