After (mostly) rebuilding my lost layout, I decided to check for module updates. Used the built-in "Add Titles" Updatifier. It found 7 updates.
It took several tries to download and install"Authorized King James Version Pure Cambridge Edition (AKJV/PCE)" and "King James Version of 1611/1769 with Strong's Numbers (KJV)." The first few times, I got an error report of unrecognized file types.
The other five downloaded and installed without incident.
However, when I accepted the "Restart Now" option, the program went unresponsive and I had to manually kill it via Task Manager. When I manually restarted it, my layout was again gone, though not as unrecoverably as before.
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I have experienced several times where TW would not respond. It had been a while since I updated resources so I had checked a bunch. When I checked fewer resources it worked fine. This is a different issue than yours, but it makes me wonder if the updater needs updating.