Is there even a way to "nuke" empty chests whitout having to check them 1 by 1? And at the same time remove the protection?
Nope. LWC needs to be removed individually or it fucks things up. You can use the MODE command to do it more easily but still...
Or... disable lwc temporarily... that would be fun, right?
For future sake, I wonder if the residence sign click to rent option may be another option to securing a shop. It would disallow theft, grief, and would be a simpler matter to disable residence to clear it for the next person to click a sign to rent. A bit more trouble on the front end to set up, may be easier to maintain. I don't know... just a possible alternative for something which may need an alternative.
Speaking of things fucked up... I see invisible chests where chests orientation had somehow been skewed. The double chests show one way while a ghost of half still inhabits the original location.