I'm using version 3 so the tags to look for are a bit different.
ie. file_history, find_in_files, find_state, incremental_find, auto_complete, etc.
However, the biggest difference, I believe, is these tags are located in two places in the same file.
Firstly they are nested under the "settings": tag.
They are also under the "windows": tag further down the file.
Not having checked a version 2 file I am not 100% sure they also aren't listed twice.
So you should probably delete the same lines from each section. Not sure what would result from mismatched histories.
Doesn't appear to have messed up my setup.
Having tried this, at least for me, it doesn't work. With just Notepad, making sure ST3 was not loaded, I cleared all the entries for the 'find history'. The file was clear of any references to any of my recent searches. Upon starting ST3, ALL the previously deleted searches were back.
Clearly there are some other places on the system that store these details.
I must have done something wrong before because it works as expected.
Clear the data in both sections and history is cleared.
I don't know why I thought it would be stored elsewhere, paranoid I guess. All those other programs writing stupid stuff to the registry. I should have realised that a cross-platform program as good as this one, would make things like this as easy as possible.