My repo is destroyed by github desktop or other software

I am using GitHub Desktop to manage my C project.

I happened twice now the Github desktop recognizes the third party project instead of my original repo.
Both occur at some random moment. I have to redo clone and do manual recovery.

Even I delete the third party project completely.
It still shows other’s project’s name and reminds me I have no write access to their repo.

The project structure is like below.

my project
           |
           - other project with .git