While converting multiple AI layers to shape layers in AE, they go invisible

Generally, converting a Vector Layer to a Shape layer is a waste of time. There is little to gain, and complex shape layers take longer to render than AI files. 

Here's what you lose: Brush Strokes, Gradients, Raster Effects (drop shadows), Blends, and a bunch of other things. 

The only legitimit reasons to convert a Vector (AI) layer to a Shape Layer:

• You are using the C4D rendering engine to extrude a shape layer
• You must animate the actual vector path
• You must use a vector path as a motion path (requires adding a null, parenting the null to the layer with the new motion path, then moving the null to a position of 0, 0 before the motion path will match the converted shape layer path)
• You need to use Shape Layer animators like Trim Paths, Offset Paths, Repeater, or other Shape Layer animators
• You need to add one or more gradient fills that can be animated (requires starting with a Vector Layer with a solid fill)

That's about it. 

If your converted layers originally contained Gradients or other unsupported features, they will get replaced with a gray fill. Select the problem layers one at a time, press the U key twice to reveal all modified properties, and you will see a bunch of groups and paths. You'll have to go through the improperly prepared layers and reorganize everything, add new gradients, and do what you can to replicate brush strokes. There is no bug reported. You are just trying to use unsupported features.