To do this, close all documents (but keep InDesign open).
Now add any colours you like. You will find that any new documents you create will include those colours.
Oh my gosh, it is that easy ... Why couldn't I figure that out! THANKS!
Don't forget you can also use Creative Cloud Libraries to store your colours.
What happens when inDesign crashes is that the preferences are reset and you lose your presets.
Make sure to Export your swatches to an ASE file so you can easily import them again.
And store them on the cloud for convenience!
To put stuff in the cloud, you've got to have cloud and we don't.
But it's OK, I don't have many presets so if inDesign ever crashes, it's not days work to enter them again.
Exporting them to an ASE file might be a good idea though.