IOS append not working?

When I try to build for IOS using the "append" option, I get the following error:

 ArgumentException: An element with the same key already exists in the dictionary.
 System.Collections.Generic.Dictionary`2[System.String,UnityEditor.iOS.Xcode.PBX.PBXFileReference].Add (System.String key, UnityEditor.iOS.Xcode.PBX.PBXFileReference value) (at /Users/builduser/buildslave/mono-runtime-and-classlibs/build/mcs/class/corlib/System.Collections.Generic/Dictionary.cs:404)
 UnityEditor.iOS.Xcode.PBXProject.RefreshMapsForGroupChildren (System.String projectPath, System.String realPath, PBXSourceTree realPathTree, UnityEditor.iOS.Xcode.PBX.PBXGroup parent)
 UnityEditor.iOS.Xcode.PBXProject.RefreshMapsForGroupChildren (System.String projectPath, System.String realPath, PBXSourceTree realPathTree, UnityEditor.iOS.Xcode.PBX.PBXGroup parent)
 UnityEditor.iOS.Xcode.PBXProject.RefreshAuxMaps ()
 UnityEditor.iOS.Xcode.PBXProject.ReadFromStream (System.IO.TextReader sr)
 UnityEditor.iOS.Xcode.PBXProject.ReadFromString (System.String src)
 UnityEditor.iOS.Xcode.PBXProject.ReadFromFile (System.String path)
 UnityEditor.iOS.PostProcessiPhonePlayer.BuildXCodeProject (UnityEditor.iOS.ProjectPaths paths, UnityEditor.iOS.IncludedFileList includedFiles, System.Collections.Generic.List`1 frameworks, System.String sdkVersion, System.String targetOS, System.String productName, Boolean useIl2Cpp, Boolean installInBuildFolder, Boolean useSymlinks, Boolean isGameCenterUsed)
 UnityEditor.iOS.PostProcessiPhonePlayer.PostProcess (UnityEditor.iOS.iOSBuildPostprocessor pp, BuildTarget target, System.String stagingAreaData, System.String stagingArea, System.String stagingAreaDataManaged, System.String playerPackage, System.String installPath, System.String companyName, System.String productName, BuildOptions options, UnityEditor.RuntimeClassRegistry usedClassRegistry)
 UnityEditor.iOS.iOSBuildPostprocessor.PostProcess (BuildPostProcessArgs args)
 UnityEditor.PostprocessBuildPlayer.Postprocess (BuildTarget target, System.String installPath, System.String companyName, System.String productName, Int32 width, Int32 height, System.String downloadWebplayerUrl, System.String manualDownloadWebplayerUrl, BuildOptions options, UnityEditor.RuntimeClassRegistry usedClassRegistry) (at /Users/builduser/buildslave/unity/build/Editor/Mono/BuildPipeline/PostprocessBuildPlayer.cs:316)
 UnityEditor.HostView:OnGUI()

I have tried using the IL2CPP scripting backend option as suggested by this answer, and it did not make any difference.

It is important that I can use the append option because my project requires me to add files and set flags in xcode and I would really rather not do all of that every time I make a build.

Any help with this would be greatly appreciated!