You can have as many masks on a layer as you want. What are you trying to do? Why did you convert the .ai layers to shape layers. There are only a couple of reasons to do so and most of the time it's not necessary. If all you want to do is generate a matte (mask) then use the original AI layer as a track matte.
It's hard to give you pointers when there are about a zillion ways to use a path and we don't have any idea what you are trying to accomplish.
I'm trying to make my ai image transform into a rectangle mask of a solid as it's shown here How to Morph Shapes in After Effects : After Effects Made Easy - YouTube So my image also needs to be a mask. Then I tried to find out how to make it a mask. The option I found involved transforming it to a shape and then pasting it's path to a placeholder mask. This is a source Convert a shape path to a mask path , yours by the way. But I can't do it with multiple paths.
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I'm trying to make my ai image transform into a rectangle mask of a solid
you can, but you don't necessarily have to. it all depends what is more suited for your workflow but mask path and shape path behave the same.
your Ai image contains vector data that can be accessed if you convert it to a shape layer by right clicking on the vector layer and choosing "Create Shapes from Vector Layer". each path you have in the illustrator art will be converted to a shape group containing a path,stroke,fill and transform property. if you need to have them all as a one single path you have to prepare your artwork beforehand in illustrator (knowing that each path will be in a separate group).
after you have successfully converted your artwork into manageable sections, now you can set a keyframe for the path property, set another for the a rectangle shape if you want - make sure you are animating the shape properly by choosing the right first vertex and even reverse direction if needed (more information in a recent thread: Re: Shape (stroke) morph causes weird flip? Set First Vertex screws up path? ) and there you go.
if you are still struggling with this please show some screenshots of the morph you want to make.