UnityEventFilter interferes with non-VRCSDK related components, causing UnityEvents to be wiped out on any object in the scene if they target forbidden types, methods or objects.
I'm heavily relying on UnityEvents for build actions, making the creator workflow significantly easier by allowing the utilization of several build time callbacks to invoke UnityEvents, however, UnityEventFilter's overzealous reach breaks this functionality for no apparent reason.
I would suggest comparing the list of components for filtering against the already existing component whitelist that exists in the SDK, since the build action components will be removed on build regardless, they just need to exist for the duration of the scene processing to get their job done, after which they are not a concern in the scope of the scene to be uploaded.
As far as I'm aware this problem exists in all versions of the SDK where UnityEventFilter is in use.
[UnityEventFilter] Events on 'X' were removed because one of them targeted a prohibited type 'X', method 'Y' or object 'X'.
UnityEngine.Debug:LogWarning (object,UnityEngine.Object)
VRC.Core.Logger:LogWarning (string,string,UnityEngine.Object)
VRC.Core.UnityEventFilter:LogRemoval (string,UnityEngine.Object) (at ./Packages/com.vrchat.worlds/Runtime/VRCSDK/SDK3/UnityEventFilter.cs:442)
VRC.Core.UnityEventFilter:FilterUnityEvents (System.Collections.Generic.HashSet`1<object>,VRC.Core.UnityEventFilter/TypeInfo,object,UnityEngine.Component) (at ./Packages/com.vrchat.worlds/Runtime/VRCSDK/SDK3/UnityEventFilter.cs:360)
VRC.Core.UnityEventFilter:FilterUnityEvents (System.Collections.Generic.ICollection`1<UnityEngine.Component>) (at ./Packages/com.vrchat.worlds/Runtime/VRCSDK/SDK3/UnityEventFilter.cs:322)
VRC.Core.UnityEventFilter:FilterUnityEvents (System.Collections.Generic.List`1<UnityEngine.GameObject>) (at ./Packages/com.vrchat.worlds/Runtime/VRCSDK/SDK3/UnityEventFilter.cs:278)
VRC.Core.UnityEventFilter:FilterEvents (System.Collections.Generic.List`1<UnityEngine.GameObject>) (at ./Packages/com.vrchat.worlds/Runtime/VRCSDK/SDK3/UnityEventFilter.cs:254)
VRC.Core.UnityEventFilter:RunFilteringOnPlayModeEntry (UnityEditor.PlayModeStateChange) (at ./Packages/com.vrchat.worlds/Runtime/VRCSDK/SDK3/UnityEventFilter.cs:125)
UnityEditor.EditorApplication:Internal_PlayModeStateChanged (UnityEditor.PlayModeStateChange)