diff --git a/v03_pipeline/lib/misc/family_entries.py b/v03_pipeline/lib/misc/family_entries.py
index b3f3c2b50..1088ae408 100644
--- a/v03_pipeline/lib/misc/family_entries.py
+++ b/v03_pipeline/lib/misc/family_entries.py
@@ -98,13 +98,17 @@ def remove_family_guids(
     family_guids: hl.SetExpression,
 ) -> hl.Table:
     # Remove families from the existing project table structure (both the entries arrays and the globals are mutated)
-    family_indexes_to_keep = hl.array(
+    family_indexes_to_keep = hl.set(
         hl.enumerate(ht.globals.family_guids)
         .filter(lambda item: ~family_guids.contains(item[1]))
         .map(lambda item: item[0]),
     )
     ht = ht.annotate(
-        family_entries=family_indexes_to_keep.map(lambda i: ht.family_entries[i]),
+        family_entries=(
+            hl.enumerate(ht.family_entries)
+            .filter(lambda item: family_indexes_to_keep.contains(item[0]))
+            .map(lambda item: item[1])
+        ),
     )
     return ht.annotate_globals(
         family_guids=ht.family_guids.filter(
diff --git a/v03_pipeline/lib/misc/lookup.py b/v03_pipeline/lib/misc/lookup.py
index 6a7e3cbbc..03a696ce3 100644
--- a/v03_pipeline/lib/misc/lookup.py
+++ b/v03_pipeline/lib/misc/lookup.py
@@ -128,22 +128,22 @@ def remove_project(
     existing_project_guids = hl.eval(ht.globals.project_guids)
     if project_guid not in existing_project_guids:
         return ht
-    project_indexes_to_keep = (
+    project_indexes_to_keep = hl.set(
         hl.enumerate(existing_project_guids)
         .filter(lambda item: item[1] != project_guid)
-        .map(lambda item: item[0])
+        .map(lambda item: item[0]),
     )
     ht = ht.annotate(
         project_stats=(
-            project_indexes_to_keep.map(
-                lambda i: ht.project_stats[i],
-            )
+            hl.enumerate(ht.project_stats)
+            .filter(lambda item: project_indexes_to_keep.contains(item[0]))
+            .map(lambda item: item[1])
         ),
     )
     ht = ht.filter(hl.any(ht.project_stats.map(hl.is_defined)))
     return ht.annotate_globals(
-        project_guids=project_indexes_to_keep.map(
-            lambda i: ht.project_guids[i],
+        project_guids=ht.project_guids.filter(
+            lambda p: p != project_guid,
         ),
         project_families=hl.dict(
             ht.project_families.items().filter(lambda item: item[0] != project_guid),