diff --git a/.github/workflows/untrustedPR.yml b/.github/workflows/untrustedPR.yml
index a58aa11219..4bbc8b2d4a 100644
--- a/.github/workflows/untrustedPR.yml
+++ b/.github/workflows/untrustedPR.yml
@@ -61,11 +61,13 @@ jobs:
           # reset the version database to the state of the merge base, so that we can check that the PR only adds one version and doesn't modify any existing versions
           git restore --source=$merge_base --staged --worktree -- versions
           git clean -fd -- versions
+          echo '{"default": {}}' > versions/baseline.json # to allow deindexing, let x-add-version completely regenerate the baseline json
           # check for version format errors separately by running x-add-version --all, recording problems it generates
           ./vcpkg x-add-version --all | grep -E '^warning:|instead of "version-string"' | tee .github-pr.version-string.out || true
           # reset the version database again
           git restore --source=$merge_base --staged --worktree -- versions
           git clean -fd -- versions
+          echo '{"default": {}}' > versions/baseline.json
           # check that the PR only adds one version and doesn't modify any existing versions, ignoring any of the warnings recorded into .github-pr.version-string.out
           ./vcpkg x-add-version --all --skip-version-format-check | tee .github-pr.x-add-version.out || true
           git add -A -- versions
diff --git a/versions/baseline.json b/versions/baseline.json
index cedd848966..69389fd6e4 100644
--- a/versions/baseline.json
+++ b/versions/baseline.json
@@ -416,10 +416,6 @@
       "baseline": "0.5.1",
       "port-version": 0
     },
-    "autobahn": {
-      "baseline": "20.8.1",
-      "port-version": 2
-    },
     "autodock-vina": {
       "baseline": "1.2.7",
       "port-version": 0
@@ -896,10 +892,6 @@
       "baseline": "1.90.0",
       "port-version": 1
     },
-    "boost-compatibility": {
-      "baseline": "1.86.0",
-      "port-version": 0
-    },
     "boost-compute": {
       "baseline": "1.90.0",
       "port-version": 1
@@ -1436,10 +1428,6 @@
       "baseline": "1.90.0",
       "port-version": 1
     },
-    "boost-vcpkg-helpers": {
-      "baseline": "1.84.0",
-      "port-version": 0
-    },
     "boost-vmd": {
       "baseline": "1.90.0",
       "port-version": 1
@@ -2040,10 +2028,6 @@
       "baseline": "9.0.1",
       "port-version": 0
     },
-    "cpp-netlib": {
-      "baseline": "0.13.0",
-      "port-version": 10
-    },
     "cpp-peglib": {
       "baseline": "1.10.2",
       "port-version": 0
@@ -2832,10 +2816,6 @@
       "baseline": "ca7cb332011ec37",
       "port-version": 1
     },
-    "etcd-cpp-apiv3": {
-      "baseline": "0.15.4",
-      "port-version": 3
-    },
     "ethindp-prism": {
       "baseline": "0.11.6",
       "port-version": 0
@@ -3180,10 +3160,6 @@
       "baseline": "3.18.0",
       "port-version": 27
     },
-    "freeopcua": {
-      "baseline": "20190125",
-      "port-version": 9
-    },
     "freerdp": {
       "baseline": "3.25.0",
       "port-version": 0
@@ -3300,10 +3276,6 @@
       "baseline": "2024-11-03",
       "port-version": 0
     },
-    "gazebo": {
-      "baseline": "11.15.1",
-      "port-version": 0
-    },
     "gcem": {
       "baseline": "1.18.0",
       "port-version": 0
@@ -6500,10 +6472,6 @@
       "baseline": "7.0.3",
       "port-version": 0
     },
-    "microsoft-signalr": {
-      "baseline": "0.1.0-alpha4",
-      "port-version": 12
-    },
     "microsoft-windows-devices-midi2": {
       "baseline": "1.0.13-preview.13.192",
       "port-version": 0
@@ -6988,10 +6956,6 @@
       "baseline": "1.69.0",
       "port-version": 0
     },
-    "nghttp2-asio": {
-      "baseline": "2022-08-11",
-      "port-version": 2
-    },
     "nghttp3": {
       "baseline": "1.15.0",
       "port-version": 0
@@ -8520,10 +8484,6 @@
       "baseline": "1.5",
       "port-version": 0
     },
-    "quickfast": {
-      "baseline": "1.5",
-      "port-version": 5
-    },
     "quickfix": {
       "baseline": "1.15.1",
       "port-version": 9
@@ -9400,10 +9360,6 @@
       "baseline": "4.0.3",
       "port-version": 3
     },
-    "socket-io-client": {
-      "baseline": "2023-11-11",
-      "port-version": 0
-    },
     "sockpp": {
       "baseline": "1.0.0",
       "port-version": 2