I’ve sort of solved my own issue, but it’s pretty hacky.
In my stun Gameplay Effect, I added a Conditional Gameplay Effect that applies a separate Gameplay Effect – we’ll call it GE_InvulnStackRemove
GE_InvulnStackRemove has an Application Requirement of the invulnerability tag, we’ll say Combat.State.Buff.Invuln
GE_InvulnStackRemove also has a Remove Gameplay Effects with Tags entry for the tag the stun Gameplay Effect adds. We’ll call it Combat.State.Debuff.Stun
Lastly, GE_InvulnStackRemove has a Granted Ability GA_RemoveInvulnStack, which is setup to activate when granted (See the GAS Documentation here to do this.) This Gameplay Ability then removes a stack of any Gameplay Effect with the tag Combat.State.Buff.Invuln
NOTE: GE_InvulnStackRemove must have its Duration Policy set to Has Duration or Infinite in order to grant a Gameplay Ability. I set mine to Has Duration and set the duration to 0.1
It’s really convoluted but it works for my purposes.