ArcGIS 10.4 has a new tool (this used to be the workstation command REBOX). It finally has made it to ArcGIS! It's funny how some things got left behind, and 15 years later we didn't know how much we missed it.
Recalculate Feature Class Extent—Help | ArcGIS for Desktop
If you have previous versions I found a workaround on Stack Exchange: Compress and uncompress the geodatabase.