There’s no need to overwrite the default preset.
You have to select your preset in the options window, not the zone window.
If you go to options => import and select your “preset X” for “Zone Templates - Single Sample” and “Zone Template - Multiple Samples”, it stays that way until you change it. No need to select it for each import.
Mine doesn’t seem to save sample quality either. It saves all else though… right down to mod matrix setup.
If you have the root entry selected in the program tree and change sample quality, it does so for all samples at once though. That does help a bit.
As far as sample loop settings are concerned - I feel your pain.
Bulk sample editing in Halion is limited or sometimes buggy.
I have found though that if you want to make bulk changes in the sample editor, you need to physically select all the samples, not just the program tree root or the layer name. This doesn’t work for loop length though.