diff --git a/agent-setup/scripts/setup.sh b/agent-setup/scripts/setup.sh
index 05eca78..b73a550 100755
--- a/agent-setup/scripts/setup.sh
+++ b/agent-setup/scripts/setup.sh
@@ -9,10 +9,24 @@ die() { echo "ERROR: $*" >&2; exit 1; }
 # so we mirror that structure under AGENT_HOME
 export GH_CONFIG_DIR="$AGENT_HOME/.github"
 
-# Write to a session dotfile so child processes inherit the variables
 mkdir -p "$AGENT_HOME"
-cat > "$AGENT_HOME/.env" <<EOF
-export GH_CONFIG_DIR="$GH_CONFIG_DIR"
-EOF
+_ENV_FILE="$AGENT_HOME/.env"
+
+# If .env exists, source it first so we preserve existing variables
+if [[ -f "$_ENV_FILE" ]]; then
+  set -a
+  source "$_ENV_FILE"
+  set +a
+fi
+
+# Update or add GH_CONFIG_DIR export
+if grep -q '^export GH_CONFIG_DIR=' "$_ENV_FILE" 2>/dev/null; then
+  # Replace existing value in place
+  sed -i.bak "s|^export GH_CONFIG_DIR=.*|export GH_CONFIG_DIR=\"$GH_CONFIG_DIR\"|" "$_ENV_FILE"
+  rm -f "$_ENV_FILE.bak"
+else
+  # Append new export
+  printf 'export GH_CONFIG_DIR="%s"\n' "$GH_CONFIG_DIR" >> "$_ENV_FILE"
+fi
 
 echo "GH_CONFIG_DIR set to $GH_CONFIG_DIR"