The accounts who already own Glowforges won’t have their file storage limited to 30 days. (That’s for machines sold after 10/31/20.)
But no, if you create a Custom Setting and save it, that will remain intact. Custom Settings are not associated with a specific file, they are associated (generally) with a type of material/thickness combination. (Just like the Proofgrade settings are.)
Saves a lot of time to just go through and set them up once for each material that you normally use. Then the next time you have a new design that you want to cut on that material, it’s one click instead of having to re-key all the parameters.