I do not think Evernote should go and change your formatting behind your back.
If you create a bulleted list without checkboxes, it leaves it as a bulleted list. At a later time, if you add checkboxes to the items in the list, Evernote will convert the bulleted list to a checklist. Please note, that conversion happens the next time you view the note. It's not like autoformating where it converts a - into a bullet or a [ ] in to a checkbox. It does it behind your back and without any indication that it is doing so.
I believe that when you leave a note, it should be in the same state w