I used Litematica to make a schematic of a build. Then, in a new world, I loaded the schematic and created a placement. However, I wanted to make changes to the schematic. In Rebuild mode, I removed some blocks that I didn't want (e.g. grass, dirt, etc) and I replaced some others (e.g. changing yellow wool to yellow concrete).

However, when I exited Minecraft, then came back in, the changes I made were no longer present in the still-loaded schematic.

Is there a way to make my changes permanent, either in the schematic as loaded or in the schematic file itself?

If not, is this a feature that could be added?

You have to save the edited schematic from the Loaded Schematics list. Unfortunately in the current 1.13.2+ versions you will then need to load that modified schematic manually and create a new placement using that version. In 1.12.2 there is an option that can automatically update the placement(s) to use that modified version when you go to save a modified schematic. There might also be a separate feature at some point that would automatically switch to using an internally saved copy of a rebuilt schematic.

Note that I don't recommend overwriting the original schematic but instead ave the rebuilt copy with a different name, especially since there is currently a bug which causes the rebuilt schematics to fail to load again correctly in certain cases (depends on the number of unique block states in the schematic before and after the rebuild operations, this has been fixed in later development versions on 1.12.2).