I used to use Orbx’s FTXCentral utility to re-sort scenery layers to proper sequential order.  FTXCentral is good but have a number of cons.

FSTscenery by Steve Greenwood is an extremely helpful alternative if sorting Layer number sequence/priority is the only requirement.   It creates a new version of scenery.CFG with all areas ordered properly.  Gaps in area or layer numbers are also deleted.

The file can be downloaded from Steve’s flight-sim traveler website.