Sounds like you don't have necessary permissions to add/modify files in the Amnesia directory.
If you're lucky, your maps likely ended up here: C:\Users\<user>\AppData\Local\VirtualStore, where <user> is your User Name you are making maps on. You can copy and paste it/them from there back to your custom story's folder. If they aren't there, then you can't get the changes you made back.
To fix this problem, right click your Amnesia's redist folder (or Steam folder if you are using a Steam copy) and set the folder to not be read-only using the first picture in these instructions:
https://www.frictionalgames.com/forum/th...#pid275735
Then always run your Level Editor as an Administrator (you can ensure the Level Editor always runs as an Administrator by ticking a setting in the Compatibility properties of the Level Editor)