You could check if there perhaps would be a .json.backup with the name of the file you are unable to find.

As for the files disappearing, I'm not too sure, I haven't heard of that before. I would recommend perhaps finding the Makeplace Folder you know is the one you use, and remove the others.

Are you using the Itch.io Launcher? If so, you can locate the folder linked to Makeplace Through the Icon next to the Launch button. 

For more steady support, please do consider joining the Makeplace server!