diff --git a/packaging/flatpak/io.unom.Punktfunk.yml b/packaging/flatpak/io.unom.Punktfunk.yml
index 6f27c165..b1d6a017 100644
--- a/packaging/flatpak/io.unom.Punktfunk.yml
+++ b/packaging/flatpak/io.unom.Punktfunk.yml
@@ -251,12 +251,19 @@ modules:
         url: https://github.com/ValveSoftware/gamescope.git
         # KEEP IN SYNC with `_gsrev` in packaging/gamescope/PKGBUILD.
         commit: 8c676c399c761e4540587f61004c957993d12fea
-      # Submodule + wrap pins as of that rev. `git ls-tree <rev> subprojects/` for the
-      # submodules; subprojects/*.wrap for the rest.
-      - type: git
-        url: https://github.com/Joshua-Ashton/vkroots.git
-        commit: 5106d8a0df95de66cc58dc1ea37e69c99afc9540
-        dest: subprojects/vkroots
+      # Wrap pins as of that rev (`subprojects/*.wrap`). These are meson WRAPS, not gamescope
+      # submodules, so nothing else populates them and they need explicit sources.
+      #
+      # vkroots is deliberately NOT listed here. It is a real gamescope SUBMODULE, and
+      # flatpak-builder clones git sources with submodules by default — so it is already
+      # checked out at exactly the rev above (`git ls-tree <rev> subprojects/vkroots`), which
+      # leaves `subprojects/vkroots/.git` as a gitlink FILE. Declaring it again with
+      # `dest: subprojects/vkroots` made the extractor copy the bare mirror onto that path and
+      # die before any build command ran:
+      #   cp: cannot overwrite non-directory '.../subprojects/vkroots/.git' with directory
+      # Re-adding it re-breaks the whole flatpak. If the submodule ever needs to be pinned away
+      # from the gamescope rev, set `disable-submodules: true` on the source above and then
+      # declare ALL THREE subprojects explicitly — not one of them alone.
       - type: git
         url: https://github.com/g-truc/glm.git
         commit: 0af55ccecd98d4e5a8d1fad7de25ba429d60e863