How to break apart vectors quickly and correctly?

I import a bunch of vectors (.ai files), but after publishing, there is a huge images folder created, the publishing speed is slowed down, the performance is affected, and there is also a problem with interacting with objects that are vectors if the HTML5 file is run directly (as opposed to publishing and running from Animate CC).

The solution to this that I've found is to break apart all the vectors into shapes. However, the order of the layers gets changed as I am breaking them apart. Now, it can be done that the background layer is broken down first, and then the foreground ones. But this is time-consuming and requires a lot of attenton to which layer is being clicked.

What is the fastest way of breaking apart vectors into shapes while retaining the order of their layers?