I haven't played HF in a while, but when wanted to play today all my previous progress was lost! When I go to %appdata%\..\LocalLow\Empyrean\House Flipper Game\ there ist no Profiles.backup. All the files were created today. Could there be something in the Steam Cloud? Is there any way to get back my progress?

All the files with today's date suggest that Steam Cloud may have asked if you'd like to upload the files stored on your PC or download a Steam Cloud save which may have been an empty default one and you accidentally chose the second option. Alternatively, in the past, we've seen some issues with windows updates doing something with %appdata% and occasionally clearing it completely.

If the backup folder is absent, I don't think there's anything else you can do in this case :C