Each save file is its own flowchart! The game autosaves all progress.
If you enter a new file, you should be able to select your choices in the visual novel itself until you have selected all options that change TRUST values. From that point on, you will be able to select choices on the flowchart itself (this is to prevent people switching options but never seeing the event that happens after they pick an option). The help button on the flowchart explains how the flowchart works, hopefully it may be of further help!