I spend a lot of time digging around in the innards. I try to solve problems by understanding how things work. (It's probably against the rules.) That means I look (but don't touch!) inside set up files like everywhere in arcgisportal/content/items/* and all the JSON files that are maintained as part of a Web AppBuilder app.
Last week it was "pagx" files that are part of my print layouts stored in Server. So, arcgisserver/directories/*
A younger more naive version of myself would say "just do a global search and repair" but experience has taught me it would really be "global search and destroy".
Ye be at the Edge! Here there be dragons!