The AuraManager is a cache that keeps the add and multiply bonuses of auras stored in order to improve performance.
It stores the classes array of the auras, for instance ["Structure", "Ship"].
In rP20737 / D1108 the DataTemplateManager component was removed and with it the serialization of aura templates in the Auras component.
So the affected classes in the AuraManager are serialized while the affected classes in the Auras component isn't serialized.
So when AuraManager.RemoveTemplateBonus is called after deserialization, that function fails to identify the old classes array, since it has a new array after deserialization.
There are multiple ways to address the issue:
(1) One would be using the Auraname as an identifier and then looking up the affected classes.
But that would be a big rewrite and we should now find the smallest bugfix (so that in case the big rewrite fails, we don't have to revert two rewrites).
(Also the performance would have to be judged)
The approach here is to not store the affected classes array, but to store the effects per item of that array.
That means the cache gets bigger, but the performance shouldn't be much worse.
The only bad part is the [class] array construction.
(3) We could change the aura template structure or MatchClasses. But that doesn't sound minimal either.