Effects Rack VS Track Effects

Let's see if we can do this in straightforward terms:

Waveform editing is destructive - you open a file, and any changes you make to it are made permanent when you save it. If you make a selection from within a file and apply an effect to it, you can't undo this once you've saved the file.

Multi-track editing is non-destructive; you aren't editing any audio files at all. What you do when you place a clip onto a track is a selective playback of it. If you trim the clip at the ends, then you are playing less of it - but it doesn't alter the fact that you have done nothing to the original file at all. So any effects added are simply applied to the playback of that clip. They aren't permanent unless you take deliberate steps to make them so. Because of the nature of this, it's possible to apply an effect either to a whole track of clips (A track effect) or just to an individual clip in the track (a clip effect). When you save the session, a session file is created, and that indicates what files are used, where they go, and what effects are applied - but this contains no audio whatsoever.

To make a permanent file of your multi-track mix, you either have to mix it down to one, or export it. When you've done this, that file becomes the permanent copy of it. If you want to make alterations to that, you have to go back to the multi-track mix, make the alterations, and save it again.

HTH