They keyboard assignments should be saved across sessions, though, without having to explicitly save the key mappings to disk. Same for the brushes.
I just ran a quick test, modifying a key assignment and made a custom brush that I saved to a bin, without saving the project, and then closed the app. Both were there after restarting TVP 10.0.4. Wondering if your crashing problems are contributing to the issue. Maybe TVPaint is reverting to a previous configuration?