Was soloing volgoth in the shattered throne last night, and when I would use my Well for damage phase my weapons would only auto reload for a few seconds, even if my Well had over 10 seconds left. There wasn't a single run when this didn't happen, almost had to fall back to Whisper.
It appeared to happen after getting hit by a few barrages of the axion darts, even though I never left the Well (it was continually healing/buffing my weapons) . The lunafaction perk would simply stop activating, and I'd have to reload like normal.
Not sure if relevant but I was running Malfeasance, Age Old Bond, and Bad Omens. It would stop reloading Malfeasance, but that might be because that was my main boss dps weapon and I always was using it at this point. Then, it wouldn't reload my other two.
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Well of radiance and lunafaction has a hard time when you are the owner of the well. Happened to us in the raid where someone else drops a well and I would have Lunafaction on.