diff --git a/sysupdate.sh b/sysupdate.sh
index 615a18b..9179bd4 100755
--- a/sysupdate.sh
+++ b/sysupdate.sh
@@ -616,15 +616,30 @@ sync_configs() {
         [[ "$skip" == true ]] && continue
 
         if [[ "$name" == "hypr" ]]; then
-            # Copy hypr/ contents but preserve ~/.config/hypr/usr/
+            # Copy hypr/ contents but preserve ~/.config/hypr/usr/.
+            # Stage each item into a temp dir on the same filesystem, then mv it
+            # into place — for files this is an atomic rename(2), so Hyprland's
+            # live config watcher never sees hyprland.lua momentarily missing
+            # (which otherwise makes it emit its fallback hyprland.conf stub).
             mkdir -p "$target/hypr"
             local hypr_ok=true
-            while IFS= read -r -d '' hitem; do
-                local hname; hname="$(basename "$hitem")"
-                [[ "$hname" == "usr" ]] && continue
-                rm -rf "${target}/hypr/${hname}" && cp -r "$hitem" "$target/hypr/" \
-                    || hypr_ok=false
-            done < <(find "$item" -maxdepth 1 -mindepth 1 -print0 | sort -z)
+            local stage; stage="$(mktemp -d "${target}/hypr/.sync.XXXXXX")" || hypr_ok=false
+            if $hypr_ok; then
+                while IFS= read -r -d '' hitem; do
+                    local hname; hname="$(basename "$hitem")"
+                    [[ "$hname" == "usr" ]] && continue
+                    if cp -r "$hitem" "$stage/"; then
+                        # mv can't atomically replace a non-empty dir, so clear
+                        # an existing directory target first; files swap atomically.
+                        [[ -d "$stage/$hname" && -d "${target}/hypr/${hname}" ]] \
+                            && rm -rf "${target}/hypr/${hname}"
+                        mv -f "$stage/$hname" "${target}/hypr/${hname}" || hypr_ok=false
+                    else
+                        hypr_ok=false
+                    fi
+                done < <(find "$item" -maxdepth 1 -mindepth 1 -print0 | sort -z)
+                rm -rf "$stage"
+            fi
             if $hypr_ok; then
                 ok "synced  hypr  ${DI}(usr/ preserved)${RS}"
                 (( synced++ )) || true