diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index f867b8f8..401e0180 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -99,7 +99,7 @@ jobs:
         run: |
           # Start postgres
           sudo su postgres -c "PG_VERSION=$PG_VERSION RUN_TESTS=0 ./ci/scripts/run-tests-linux.sh" && \
-          sudo su -c "cd /tmp/lantern && PG_VERSION=$PG_VERSION ./lantern_hnsw/cienv/bin/python ./lantern_hnsw/scripts/test_updates.py -U postgres --builddir ./lantern_hnsw/build_updates --rootdir ./lantern_hnsw" &&\
+          sudo su -c "cd /tmp/lantern/lantern_hnsw && PG_VERSION=$PG_VERSION ./cienv/bin/python ./scripts/test_updates.py -U postgres --builddir ./build_updates --rootdir ." &&\
           echo "Done with updates"
         env:
           PG_VERSION: ${{ matrix.postgres }}
diff --git a/lantern_hnsw/scripts/test_updates.py b/lantern_hnsw/scripts/test_updates.py
index 6fa67011..d1d3456a 100644
--- a/lantern_hnsw/scripts/test_updates.py
+++ b/lantern_hnsw/scripts/test_updates.py
@@ -92,6 +92,9 @@ def update_from_tag(from_version: str, to_version: str, starting_point  = None):
         if not "error: cannot run ssh" in str(e):
             raise Exception(f"unknown fetch error: {e}")
 
+    rootdir = args.rootdir
+    if Version(from_version) < Version("0.3.5"):
+        rootdir = ".."
 
     sha_after = repo.head.object.hexsha
     print(f"Updating from tag {from_tag}(sha: {sha_after}) to {to_version}")
@@ -100,8 +103,13 @@ def update_from_tag(from_version: str, to_version: str, starting_point  = None):
     # checkout to latest to make sure we always run the latest version of all scripts
     repo.git.checkout(from_tag)
     # run "mkdir build && cd build && cmake .. && make -j4 && make install"
-    res = shell(f"mkdir -p {args.builddir} ; git submodule update --init --recursive && cmake -DRELEASE_ID={from_version} -S {args.rootdir} -B {args.builddir} && make -j install")
+    res = shell(f"rm -rf {args.builddir} || true")
+    res = shell(f"mkdir -p {args.builddir} ; git submodule update --init --recursive && cmake -DRELEASE_ID={from_version} -S {rootdir} -B {args.builddir} && cd {args.builddir} && make -j install")
     repo.git.checkout(starting_sha)
+    # We are just compilinig again (not installing)
+    # Because file structure was changed afte 0.3.5 version 
+    # And cmake complains that CMakeFiles does not exist
+    res = shell(f"rm -rf {args.builddir} third_party && mkdir -p {args.builddir} && git submodule update --init --recursive && cmake -DRELEASE_ID={from_version} -S {args.rootdir} -B {args.builddir} && cd {args.builddir} && make -j")
 
 
     res = shell(f"psql postgres -U {args.user} -c 'DROP DATABASE IF EXISTS {args.db};'")
@@ -121,7 +129,7 @@ def update_from_tag(from_version: str, to_version: str, starting_point  = None):
     res = shell(f"cd {args.builddir} ; UPDATE_EXTENSION=1 UPDATE_FROM={from_version} UPDATE_TO={from_version} make test-misc FILTER=begin")
 
     repo.git.checkout(to_sha)
-    res = shell(f"git submodule update --init --recursive && cmake -DRELEASE_ID={to_version} -S {args.rootdir} -B {args.builddir} && cd {args.builddir} && make -j install")
+    res = shell(f"rm -rf {args.builddir} third_party && rm -rf third_party && mkdir -p {args.builddir} && git submodule update --init --recursive && cmake -DRELEASE_ID={to_version} -S {args.rootdir} -B {args.builddir} && cd {args.builddir} && make -j install")
     repo.git.checkout(starting_sha)
 
     res = shell(f"cd {args.builddir} ; UPDATE_EXTENSION=1 UPDATE_FROM={from_version} UPDATE_TO={from_version} make test-misc FILTER=version_mismatch")
@@ -215,9 +223,3 @@ def incompatible_version(pg_version, version_tag):
             if incompatible_version(pg_version, from_tag):
                 continue
             try_update_from_tag(str(from_tag), str(latest_version))
-
-
-
-
-
-