We can't know. You have not provided exact project details, screenshots of the layers, version info, system info and so on.
I've never had a layer disappear from a timeline unless I deleted them. My first question is did you save your project and create a backup before you rendered? My second question: What, exactly, was your workflow from the time you completed your project and decided to render?
I am using:
After Effects CC Version 18.104.22.168
MacBook Pro (Retina, 15-inch, Late 2013)
OSX Yosemite 10.10.1
Memory: 16 GB 1600 MHz DDR3
Graphics: NVIDIA GeForce GT 750M 2048 MB
Screenshot of the current layers:
What you see here is a hot air balloon from the bottom. I had a rotating image hovering underneath the basket of the hot air balloon, but it is now missing without a trace. This layer was NOT the last layer that I added to my project. I had added it many steps ago, and saved/loaded my project with this layer intact many times. To render, the other day, in after effects, I selected from the top menu Composition>Add To Adobe Media Encoder Queue. I encoded it Adobe Media Encoder's default H.264/Match Source-High Bitrate Preset.
2 things: first of all, the video took a RIDICULOUS amount of time to render. About 12 hours for 1 minutes worth of footage (granted, there are some particle streams at the beginning). Also, the video came out looking incredible grainy, pixelated, and low quality (usually when I use this Adobe Media Encoder Preset, my videos come out looking great). And the biggest thing of all, I noticed in the video a few elements were missing!!! That's when I returned to my After Effects Project and noticed that this layer was just completely gone...nowhere to be found. No trace of it, that I can see. I am mystified.
Just for giggles, I rendered the same composition with After Effects internal renderer, and the video not only came out with much better resolution, but also rendered much faster.
I think Adobe Media Encoder ate my now missing layer.