I'm experiencing an issue with Adobe After Effects (version 24.5.0) where my null objects and solids randomly disappear when I close or save my project. I've also noticed that this sometimes happens after I pre-compose layers, even if those layers are unrelated to the null objects/solids. The issue doesn't occur every time I perform these actions. For instance, I might pre-compose or save to test if the bug appears, and everything will seem fine, but a couple of hours later into the project, when I pre-compose again, my null objects disappear. Sometimes I don’t notice the issue immediately, making it impossible to undo, which makes this problem even more frustrating.
What are your system specifications (CPU, GPU, RAM, OS version)? Are you getting this issue with all the files? Do the layers disappear from the composition only, Timeline only, or from both?
To follow up on @nishu_kush's response... are the Nulls and Solids also disappearing from the Project Panel? If not, can you click on either the Null or Solid in the Project Panel and see how many times it is being used in the project?
Does that number go down after one of these layers disappears after PreComping?