I recently introduced some css to User:Jdlrobson/minerva.css
As you can see now my user css is empty and was last edited 4 hours ago, but clearly the css is still being applied (indicated by green/red boxes around elements)
( for reference http://en.m.wikipedia.beta.wmflabs.org/wiki/User:Jdlrobson/minerva.css )
I suspect this is a bug in how ResourceLoader caching works.
the module providing this functionality is ResourceLoaderUserModule which only overrides getPages:
Would appreciate ResourceLoader expertise. I can replicate this on production too.