Did you have automatic backup set up? Can you reproduce this problem? I'm afraid I am not clear what you did, what does "make shorter version" mean? I have many projects I can save as .capx and they work just fine...
I have a backup1 as extension, i had no idea what is it, but i managed to rename it to remove .backup1 and i opened it, it saved my day :D!
uhhh... i was worried, so i'm glad about back up.
The problem is you need to do on following steps:
1-Create a .caproj
2-Create some layouts and some objects.
4-Delete some layouts
5-Save as single file
6-Close project (it didnt appear a window save before exit)
7-Open .caproj again