Editing a linked mesh with modifiers: workflow?

I’m making a shrub, and as a placeholder I made the trunk/branches first, and then ALT+D’d them into place, thinking I’d come back and edit in the foliage, and magically they’d all have foliage. They have SKIN+SUBD modifiers applied.

My disappointment when I couldn’t APPLY the modifiers to the original was profound.

If I wanted to do this correctly, what should I have done?
(I was able to recover gracefully with LINK DATA, but I think there must be a smoother way to do this.)