Pausing during timed phase in Abyssal Depths boss fight doesn't work properly, breaks the fight

I entered the fight, died a couple times, completed the first spire phase, died a couple more times, then got the second spire phase to start. I paused the game (timer was at 1:08) before entering the second spire's sub-arena room, then came back about 10 minutes later and the fight could not be completed.

The timer resumed when the game was unpaused.
All three spire rooms and the exit were open.
The two remaining spires were in their active animation but untargetable and not attacking.
The boss never reappeared.