Hi Darren,

1) Can fillets be edited once applied?

No

2) When you save a file, does it always go through the same process of opening up a save file dialogue and then once you've named (or copied over) the file, prompt you to set the number of polygons etc? Or can this be skipped, and simply hitting save will copy over your existing file unless you 'save as...'?

No.
The process you describe is the Export function.
In V4 (as in V3) the export function opens a save file dialog where you choose the name and the file format you want to export.
Next if the file format is based on polygons the function prompts to set the number of polygons.
But the save file function uses the native .3dm file format and is a silent function

Have fun Darren !