History is store on $(ipython locate)/profile_default/history.sqlite by default.
You can remove the file, and or do any operation you want on it (secure erase, etc..).
It’s an sqlite file so you can load it with any sqlite program and do query on it.
Check in $(ipython locate)/profile_default/ and other $(ipython locate)/profile_xxx that you do not have any other history files. $(ipython locate) is usually ~/.ipython/ but can vary:
ls $(ipython locate)/profile_*/*.sqlite