It is also happening to me with Architect 2.2.2 Build 971. Seems random. I have 3 CSS resource files and 5 js resource files. It never seems to lose more than one js file at a time. It might be happening the first time after I open the project then do my first Publish of the day. The js files are still in my runtime folder and in my project folder, the app.html file is missing the script tag for the js file and the resource is missing from the Architect project.
Windows 7 OS.
The only thing in the log is:
5/22/2013 10:12:35 AM Info Project Project successfully saved