Can I filter the records to add when I use the Copy Master Detail wizard?

This largely depends on how your application is set up, 

but most of the time you can add filtering criteria similarly to {FID.EX.Criteria}

So if your field that you want to match is field ID 10, and the match is 1. it would be {10.EX.1}

But you'd have to set up a template for it.

Just some ideas, I don't have a lot of experience using the default "Copy Master Detail" wizard

I do not think that there is an option when cinfiguring either the wizard or the API version of the Copy master detail to filter which child records get copied.

I think what I would do is to flag which records need to be deleted using the formula and then create some kind of your URL formula button on the parent which would be pushed after the copy Master Detail is done to mass delete the flag records. So it would be a two-step process.

After you use the wizard and it creates a button.
What is the formula for that button?  You might be able to put the filtering there...