Your workflow needs testing, I'm sure you agree this doesn't seem logical.
The timeframe shouldn't have anything to do with it. You describe the file not actually being saved, or saved to another location. Start a new drawing, save it and check the timestamp on the file before closing LibreCad. Try saving it to another location, maybe a usb drive.
The ~ file is a backup so it has to be an earlier version.
I have changed my saving routine. I now save the file then copy it to the cloud.
Here is what I think happened;
I opened a new page and started work. For some reason I left that unsaved and opened a 2nd drawing which I saved regularly and eventually completed.
When I closed Libracad the dialogue box came up telling me to save the original unnamed draft, it was late, I was tired so I saved it giving it the same name as my main project. I must have saved twice which is why I lost the backup. GAME OVER and lesson learnt.