I had a very similar experience: created several projects in folders with custom names and locations.
Then, cleaned my computer’s files system and all Kicad links to my stuff went to hell.
I solved it by:
- Following the file locations shown in the imaged below (which came from this Post)
- Renaming the Folders with my stuff and made darn sure to Not use non-system-wide fonts. Previously, I used a ‘Bullet’ to lead the folder name but that went south real fast.
I renamed my folders to start with the letter ‘z’ so they’d be at the bottom of the file/parts listing (for visual convenience).
Made a world of difference in my using Kicad. Now, all my stuff is as shown below…

