diff --git a/.github/workflows/db-migration-backwards-compatibility.yaml b/.github/workflows/db-migration-backwards-compatibility.yaml
index 882755384..d5798ba31 100644
--- a/.github/workflows/db-migration-backwards-compatibility.yaml
+++ b/.github/workflows/db-migration-backwards-compatibility.yaml
@@ -1,4 +1,4 @@
-name: DB migrations are backwards-compatible with main branch
+name: DB migrations are backwards-compatible
 
 on:
   push:
@@ -16,6 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     outputs:
       migrations_changed: ${{ steps.check-diff.outputs.migrations_changed }}
+      base_branch: ${{ steps.check-diff.outputs.base_branch }}
     steps:
       - name: Checkout current branch
         uses: actions/checkout@v6
@@ -25,9 +26,17 @@ jobs:
       - name: Check for migration changes
         id: check-diff
         run: |
-          # Get the merge base with main
-          git fetch origin main
-          MERGE_BASE=$(git merge-base HEAD origin/main)
+          # Determine base branch: dev compares to main, all others compare to dev
+          if [ "${{ github.ref }}" = "refs/heads/dev" ]; then
+            BASE_BRANCH="main"
+          else
+            BASE_BRANCH="dev"
+          fi
+          echo "base_branch=$BASE_BRANCH" >> $GITHUB_OUTPUT
+          
+          # Get the merge base with the base branch
+          git fetch origin $BASE_BRANCH
+          MERGE_BASE=$(git merge-base HEAD origin/$BASE_BRANCH)
           
           # Check if there are any changes in the migrations folder
           if git diff --quiet "$MERGE_BASE" HEAD -- apps/backend/prisma/migrations/; then
@@ -39,7 +48,7 @@ jobs:
           fi
 
   backwards-compatibility:
-    name: Test migrations with main branch code
+    name: Test migrations with ${{ needs.check-migrations-changed.outputs.base_branch }} branch code
     needs: check-migrations-changed
     if: needs.check-migrations-changed.outputs.migrations_changed == 'true'
     runs-on: ubicloud-standard-8
@@ -61,19 +70,19 @@ jobs:
           mkdir -p saved-migrations
           cp -r current-branch/apps/backend/prisma/migrations/* saved-migrations/
 
-      # Now checkout main branch
-      - name: Checkout main branch
+      # Now checkout base branch (main for dev, dev for all others)
+      - name: Checkout base branch
         uses: actions/checkout@v6
         with:
-          ref: main
-          path: main-branch
+          ref: ${{ needs.check-migrations-changed.outputs.base_branch }}
+          path: base-branch
 
-      # Move main-branch to the root for the rest of the workflow (keep main's migrations for now)
+      # Move base-branch to the root for the rest of the workflow (keep base's migrations for now)
       - name: Setup working directory
         run: |
           shopt -s dotglob
-          mv main-branch/* .
-          rm -rf main-branch current-branch
+          mv base-branch/* .
+          rm -rf base-branch current-branch
 
       - name: Setup Node.js
         uses: actions/setup-node@v6
@@ -187,8 +196,8 @@ jobs:
       - name: Wait 10 seconds
         run: sleep 10
 
-      # First test run: main branch with main's migrations
-      - name: Run tests (main branch with original migrations)
+      # First test run: base branch with base's migrations
+      - name: Run tests (base branch with original migrations)
         run: pnpm test
 
       # Now copy over current branch's migrations and run migrate
@@ -201,8 +210,8 @@ jobs:
       - name: Run database migrations
         run: pnpm run db:migrate
 
-      # Second test run: main branch code with new migrations applied
-      - name: Run tests (main branch with new migrations)
+      # Second test run: base branch code with new migrations applied
+      - name: Run tests (base branch with new migrations)
         run: pnpm test
 
       - name: Verify data integrity
diff --git a/apps/backend/prisma/migrations/20260201230002_env_to_branch_config/migration.sql b/apps/backend/prisma/migrations/20260201230004_env_to_branch_config/migration.sql
similarity index 85%
rename from apps/backend/prisma/migrations/20260201230002_env_to_branch_config/migration.sql
rename to apps/backend/prisma/migrations/20260201230004_env_to_branch_config/migration.sql
index a3ad60aae..c23f13895 100644
--- a/apps/backend/prisma/migrations/20260201230002_env_to_branch_config/migration.sql
+++ b/apps/backend/prisma/migrations/20260201230004_env_to_branch_config/migration.sql
@@ -178,6 +178,52 @@ END;
 $$ LANGUAGE plpgsql IMMUTABLE;
 -- SPLIT_STATEMENT_SENTINEL
 
+-- Create function to flatten nested JSONB into dot-notation
+-- e.g., {"auth": {"oauth": {"providers": {"github": {"isShared": true}}}}}
+-- becomes {"auth.oauth.providers.github.isShared": true}
+-- SPLIT_STATEMENT_SENTINEL
+-- SINGLE_STATEMENT_SENTINEL
+CREATE OR REPLACE FUNCTION temp_flatten_config(config JSONB, path_prefix TEXT DEFAULT '')
+RETURNS JSONB AS $$
+DECLARE
+  result JSONB := '{}'::jsonb;
+  key TEXT;
+  value JSONB;
+  full_path TEXT;
+  flattened_child JSONB;
+  child_key TEXT;
+  child_value JSONB;
+BEGIN
+  IF config IS NULL THEN
+    RETURN '{}'::jsonb;
+  END IF;
+
+  FOR key, value IN SELECT * FROM jsonb_each(config) LOOP
+    -- Build the full path for this key
+    IF path_prefix = '' THEN
+      full_path := key;
+    ELSE
+      full_path := path_prefix || '.' || key;
+    END IF;
+    
+    -- If value is an object, recurse and flatten
+    IF jsonb_typeof(value) = 'object' THEN
+      flattened_child := temp_flatten_config(value, full_path);
+      -- Merge all flattened child keys into result
+      FOR child_key, child_value IN SELECT * FROM jsonb_each(flattened_child) LOOP
+        result := result || jsonb_build_object(child_key, child_value);
+      END LOOP;
+    ELSE
+      -- Non-object values: add with full dot-notation path
+      result := result || jsonb_build_object(full_path, value);
+    END IF;
+  END LOOP;
+  
+  RETURN result;
+END;
+$$ LANGUAGE plpgsql IMMUTABLE;
+-- SPLIT_STATEMENT_SENTINEL
+
 -- Create temporary index to speed up the migration
 -- SPLIT_STATEMENT_SENTINEL
 -- SINGLE_STATEMENT_SENTINEL
@@ -216,7 +262,7 @@ inserted AS (
 ),
 updated AS (
   UPDATE "EnvironmentConfigOverride" eco
-  SET "config" = temp_filter_env_only_config(eco."config"),
+  SET "config" = temp_flatten_config(temp_filter_env_only_config(eco."config")),
       "updatedAt" = CURRENT_TIMESTAMP
   FROM inserted i
   WHERE eco."projectId" = i."projectId"
@@ -259,7 +305,7 @@ upserted_branch AS (
   RETURNING "projectId", "branchId"
 )
 UPDATE "EnvironmentConfigOverride" eco
-SET "config" = temp_filter_env_only_config(eco."config"),
+SET "config" = temp_flatten_config(temp_filter_env_only_config(eco."config")),
     "updatedAt" = CURRENT_TIMESTAMP
 FROM leftover_configs lc
 WHERE eco."projectId" = lc."projectId"
@@ -267,6 +313,7 @@ WHERE eco."projectId" = lc."projectId"
 -- SPLIT_STATEMENT_SENTINEL
 
 -- Clean up temporary functions
+DROP FUNCTION IF EXISTS temp_flatten_config(JSONB, TEXT);
 DROP FUNCTION IF EXISTS temp_filter_env_only_config(JSONB);
 DROP FUNCTION IF EXISTS temp_filter_branch_config(JSONB);
 DROP FUNCTION IF EXISTS temp_filter_config(JSONB, BOOLEAN, TEXT);