How do you replace the damage die for a homebrew magical weapon? For example, the damage die on the current weapon is a d6, but I want it to be a d8. How would I change this?

Can't yet.

Depending on what it is, you could always make it as something else with the appropriate die then adjust the properties accordingly. For example - I made a Bastard Sword for someone which was d10/12 (versatile) and just tweaked the properties for a glaive (d10 damage die). The only issue you may run into doing that though is weapon proficiencies but there's an option for "self". You just need to make sure the player is proficient with whatever the weapon should be, not what the system thinks it is.

This doesn't work for me. I can ignore weapon properties, but when I try to add one, nothing happens or the old properties come back.

Do you mean in the item’s editor the old modifiers disappear? Or do you mean on the character sheet?

After you save a modifier, then save the whole item as well. Usually you don’t have to do it until the end, but just to be on the safe side.... Once the weapon is on the character sheet, it should work the way you programmed it.