Setup an app variants folder and move the nightly and alpha build configs to it.

Variants/Alpha/Resources/Alpha.xcassets/AlphaAppIcon.appiconset/Contents.json

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+{
+  "images" : [
+    {
+      "filename" : "AppIcon.png",
+      "idiom" : "universal",
+      "platform" : "ios",
+      "size" : "1024x1024"
+    }
+  ],
+  "info" : {
+    "author" : "xcode",
+    "version" : 1
+  }
+}

Variants/Alpha/Resources/Alpha.xcassets/Contents.json

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+{
+  "info" : {
+    "author" : "xcode",
+    "version" : 1
+  }
+}

Variants/Alpha/alpha.yml

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+settings:
+  BASE_APP_GROUP_IDENTIFIER: io.element.pr
+  BASE_BUNDLE_IDENTIFIER: io.element.elementx.pr
+
+targets:
+  ElementX:
+    settings:
+      base:
+        ASSETCATALOG_COMPILER_APPICON_NAME: AlphaAppIcon
+    sources:
+    - path: Resources

Variants/Nightly/Resources/Nightly.xcassets/Contents.json

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+{
+  "info" : {
+    "author" : "xcode",
+    "version" : 1
+  }
+}

Variants/Nightly/Resources/Nightly.xcassets/NightlyAppIcon.appiconset/Contents.json

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+{
+  "images" : [
+    {
+      "filename" : "AppIcon.png",
+      "idiom" : "universal",
+      "platform" : "ios",
+      "size" : "1024x1024"
+    }
+  ],
+  "info" : {
+    "author" : "xcode",
+    "version" : 1
+  }
+}

Variants/Nightly/nightly.yml

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+settings:
+  BASE_APP_GROUP_IDENTIFIER: io.element.nightly
+  BASE_BUNDLE_IDENTIFIER: io.element.elementx.nightly
+
+targets:
+  ElementX:
+    settings:
+      base:
+        ASSETCATALOG_COMPILER_APPICON_NAME: NightlyAppIcon
+    sources:
+    - path: Resources