If a Confluence is copied, the effect that creates the copy will usually allow you to choose new targets, but you can't choose new modes.

If a mode requires a target, you can select that mode only if there's a legal target available. Ignore the targeting requirements for modes you don't choose. Each time you select that mode, you can choose a different target, or you can choose the same target.

If all targets for the chosen modes become illegal before a Confluence resolves, the spell will be countered and none of its effects will happen. If at least one target is still legal, the spell will resolve but will have no effect on any illegal targets.

If the same mode is chosen more than once, you choose their relative order as you cast the spell. For example, if you choose the last mode of Cosmium Confluence more than once, you choose the relative order to destroy the target enchantments.

Notably, the second mode doesn't require any targets. You choose the Cave you control that will be affected as Cosmium Confluence is resolving. You may choose a Cave you just put onto the battlefield with the first mode, if applicable.

No player can cast spells or activate abilities in between the modes of a resolving spell. Any abilities that trigger won't be put onto the stack until a spell is done resolving.

You choose the modes as you cast the spell. Once modes are chosen, they can't be changed.

No matter which combination of modes you choose, you always follow the instructions in the order they are written.