It might be a good idea to store open "Find All" panels in a project file, just like breakpoints and bookmarks, and reload and display them when the project is opened again.
Since "Find All" panels have the very convenient "Find Again" button, there could even be an option to automatically refresh the searches when the project is opened.
This would, of course, consume some time when the project is loaded, but it would be a nice way of keeping track of // TODO and // BUG comments, for example.