So after several hours of testing I think I finally figured out what is causing revenant utility skills to change "random" order.
For whatever reason legend swapping during a utility skill with cast time takes its default counter part and drags it to its slot.
For example, Riposting Shadows is default skill 1 for Shiro and Facet of Darkness is for Glint. If I cast Riposting Shadows from any skill slot and legend swap during, it will drag Facet of Darkness to that same skill slot. If I cast Burst of Strength and swap during animation it will drag Impossible Odds to that slot.
This goes for any Utility Skill with a cast time. The default 7/8/9 skills are linked to each other respectively across legends. This is why some of us are experiencing it a little occasionally and some are experiencing it A LOT.
I suspect this still has something to do with how they handled the hero panel update that allowed people to directly place their skills from their land and water sets.
A temp solution to prevent skill reordering atm is to either make sure your 2 legends 7/8/9 utility skills are "default paired" back to back (they can be in any of the 3 slots, just need to be paired) in their respective slots OR don't legend swap during a utility skill cast animation. Note that this does not affect instant cast times and is unlikely to affect 1/4 sec casts so you can attempt to work around that. I was able to bug with 1/2 sec Kalla skills though.
Ug what a mess.
The skill pairings are (tested in game),
Anet buff me :-(
Make me good at game!