I hope it's not considered forward, but as someone about to play a game with Aura of Despair I went ahead and fixed this so I could use this extension, and figured I might as well share. (I didn't see any other post saying it was fixed at least.) I also made it work with PFRPG, but that's easy (just added the xml tag and pointed it to 35E instead of 5E if DataCommon.isPFRPG). For the record I'm on FG Classic.
I'm pretty sure that effect removal wasn't working for auras with negative values because, on line 91 in checkAuraAlreadyEffecting(), it was using string.match(str, str) to check for existing auras. But string.match uses something similar to regex to match, and a minus sign is a special character for matching the shortest repeating substring or some such, so only positive values were being matched properly. I swapped that line for string.find(str, str, 1, true)
so that it would treat the second argument as a plain string instead of as a pattern and it seems happier now.
Hope I'm not being a bother/my change actually helps, and thanks for the great extension!