I may have a lead!
While doing today’s Pet Rescue, I noticed Submerged also spontaneously disappearing from enemy Troops (without spellcast, skull damage, etc) and captured video footage of it.
On closer inspection, it seems to correlate with the “auto cleanse” visual effect that is suddenly occurring to Troops that don’t actually have any status ailments. This suggests the bug is not just removing negative Status Effects (as it should), it’s possibly removing ALL status effects (including positives) ?
It doesn’t seem to impact Reflect, Enrage, or Barrier, just the effects that disappear on spellcast.