diff --git a/configs/repositories.toml b/configs/repositories.toml
index f9a7bdd3..f25b8e08 100644
--- a/configs/repositories.toml
+++ b/configs/repositories.toml
@@ -36,12 +36,14 @@ REPOSITORY = "sbo"
 
 [NEW_PACKAGES]
 # Configure the repositories that you want new packages to be added
-# when upgrading installed packages. Example ["slack", "gnome"].
+# when upgrading installed packages. Only useful for repositories that
+# are fully installed on the system. Example ["slack", "gnome"].
 REPOSITORIES = []
 
 [REMOVE_PACKAGES]
 # Configure the repositories that you want to remove installed packages
-# that no longer exist in the repository. Example ["slack", "gnome"].
+# that no longer exist in the repository. Only useful for repositories
+# that are fully installed on the system. Example ["slack", "gnome"].
 REPOSITORIES = []
 
 [SBO]
diff --git a/slpkg/repositories.py b/slpkg/repositories.py
index 0c357ef9..2ba157b1 100644
--- a/slpkg/repositories.py
+++ b/slpkg/repositories.py
@@ -31,7 +31,7 @@ class Repositories:  # pylint: disable=[R0902]
 
     repos_config = {}
     repositories = {}
-    repos_toml = {}  # type: ignore[var-annotated]
+    repos_toml = {}
 
     data_json: str = 'data.json'
     repos_information: Path = Path(repositories_path, 'repos_information.json')
@@ -444,7 +444,9 @@ class Repositories:  # pylint: disable=[R0902]
     defaults_repos = list(repositories.keys())
 
     diff_repos = list(set(all_repos) - set(defaults_repos))
-    diff_repos.remove('default')
+    items_to_remove = ('default', 'new_packages', 'remove_packages')
+    for item in items_to_remove:
+        diff_repos.remove(item)
 
     if diff_repos:
         for repo, data in repos_config.items():