Aftereffects losing layers?

When you render your composition, Render Queue panel opens at the bottom of your screen in front of your Timeline.

To go back to your layers in the Timeline, just click the name of the composition next to Render Queue panel or double-click the name of your composition in the Project panel

User Guide, that should be your first stop. 

After Effects pojects are saved as an AEP file. You use After Effects to crete visual effects and motion graphics shots that cannot be created in a video editing app like Premiere Pro. After Effects is not intended for editing videos, it is designed to create snots by layering various elements in a  compositi0n. When you render a composition you get a video. Video is not interactive and not layered. A video may have more than 3 color channels if it is the right format, but there are no layers to see.

If you want to go back and look at the composition you need to open the AEP file and look at the composition. Until you are an expert in video formats, standards, and compression, you should be using the Presets. Creating custom compositions will just get you into trouble. The most common preset is the 1920 X 1080 HD preset with a 29.97 fps frame rate in all countries that have 60Hz power (NTSC) and 25fps in countries with 50Hz power (PAL). If you use the Adobe Media Encoder to render for YouTube or any other streaming platform then you should use the presets for that platform found in the H.264 section.

Once again, don't edit video using After Effects (my average comp is under 7 seconds and one shot), don't use custom settings for comps or rendering until you know what you are doing, and spend some time with the User Guide so you don't develop bad workflow habbits and you understand the workflow and the UI. AE is complicated and if you don't do your homework you might just crash and burn.