Hello,
I had this same type of situation. I had a AI layer in a precomp, and I applied a stroke effect to it. In my Main Composition, I had a 3d camera and my precomp, but my AI layer with the stroke effect was gone (i.e., couldn’t see it anymore). If found out that if I turned off the Continuously Rasterize option on my precomp in my Main Composition that the stroke effect and my layer both appeared again. I wasn’t able to have the good vecter quality of my AI file, but in my pre-comp I just sized up my AI layers (in my pre-comp, my AI layers were all on Continuously Rasterize) until I had a good size where even if I zoomed in or out in my Main Composition, I still had good quality. This is an old post but I hope this helps anyone who may have this same problem.
AL – After Effects Animator