Shadowheart can be killed by the PC anytime. You can complete the Gauntlet without her and if she is alive she would leave. Is the cube in your inventory?
I checked the inventory of my main custom character and all the rest of the companions. I did not find the cube anywhere. I also checked the 2 merchants in the Grove to see if I sold the cube by accident (I don't think the game would allow this).
I don't know if this is related but in some of my games, during the first or second patch, if I dropped a character from my active team, my custom character would get all the bags (and the cube in the case of Shadowheart) from the dropped player placed in his inventory. When I brought the dropped character back on the team, I had to move their bags back to their inventory. Patch 2 or 3 removed this inconvenient action. This resulted in my custom character having the cube in his inventory since I could not move it back to Shadowheart.
I have about 15 hours of play in this game. I have done the Chapel ruins (Withers is available), a bunch of quests in the Grove and along the way to the Blighted Village (for instance, I have met Scratch and he is in my camp now). I have not gotten Karlach yet, nor have I met the Paladin of Tyr.
Withers mentions resurrections but does not offer a dialog to start the process. I am talking to him with 2 available slots in my group.
Unexpectedly, I must have skipped getting Wyll. He is not in my camp or the Grove (where I found him in all other games). I know I skipped getting him to join me initially. I assumed he would be continue to be available in the Grove.
As a point of information, the game characters are all at level 3.
BenC