diff --git a/rust_port/crates/flow_common/src/files.rs b/rust_port/crates/flow_common/src/files.rs
index 94f6b4e3107..90dc7f3e705 100644
--- a/rust_port/crates/flow_common/src/files.rs
+++ b/rust_port/crates/flow_common/src/files.rs
@@ -908,11 +908,12 @@ pub fn expand_project_root_token(root: &Path, s: &str) -> String {
 
 pub fn expand_project_root_token_as_relative(s: &str) -> String {
     let s = s.replace(PROJECT_ROOT_TOKEN, "");
-    if s.starts_with('/') || s.starts_with('\\') {
+    let s = if s.starts_with('/') || s.starts_with('\\') {
         s[1..].to_string()
     } else {
         s
-    }
+    };
+    normalize_filename_dir_sep(&s).into_owned()
 }
 
 pub fn expand_builtin_root_token(flowlib_dir: &Path, s: &str) -> String {
diff --git a/rust_port/crates/flow_parser/src/file_key.rs b/rust_port/crates/flow_parser/src/file_key.rs
index aea4c899fd1..d76f709eda3 100644
--- a/rust_port/crates/flow_parser/src/file_key.rs
+++ b/rust_port/crates/flow_parser/src/file_key.rs
@@ -317,12 +317,14 @@ fn relative_path_from(root: &str, path: &str) -> String {
     result.join("/")
 }
 
+// The result always uses '/' separators for cross-platform consistency
+// (saved state generated on Linux must work on Windows and vice versa).
 pub fn strip_project_root(path: &str) -> String {
     let guard = PROJECT_ROOT.read().unwrap();
     match guard.as_deref() {
         Some(root) => {
             if let Some(stripped) = path.strip_prefix(root) {
-                stripped.to_string()
+                normalize_dir_sep_with(std::path::MAIN_SEPARATOR, stripped)
             } else if !is_relative(path) {
                 relative_path_from(root, path)
             } else {
@@ -437,7 +439,9 @@ impl FileKey {
         let guard = FLOWLIB_ROOT.read().unwrap();
         let suffix = match guard.as_deref() {
             Some(fl) if !fl.is_empty() && path.starts_with(fl) => {
-                format!("{}{}", FLOWLIB_MARKER, strip_prefix(fl, path))
+                let stripped =
+                    normalize_dir_sep_with(std::path::MAIN_SEPARATOR, strip_prefix(fl, path));
+                format!("{}{}", FLOWLIB_MARKER, stripped)
             }
             _ => {
                 drop(guard);
diff --git a/src/common/files.ml b/src/common/files.ml
index 65b5e119302..3a777dec68c 100644
--- a/src/common/files.ml
+++ b/src/common/files.ml
@@ -1031,10 +1031,13 @@ let expand_project_root_token_as_absolute ~root =
 
 let expand_project_root_token_as_relative str =
   let s = str |> Str.split_delim project_root_token |> String.concat "" in
-  if String.length s > 0 && (s.[0] = '/' || s.[0] = '\\') then
-    String.sub s 1 (String.length s - 1)
-  else
-    s
+  let s =
+    if String.length s > 0 && (s.[0] = '/' || s.[0] = '\\') then
+      String.sub s 1 (String.length s - 1)
+    else
+      s
+  in
+  Sys_utils.normalize_filename_dir_sep s
 
 let expand_builtin_root_token ~flowlib_dir =
   let flowlib_dir_str = File_path.to_string flowlib_dir |> Sys_utils.normalize_filename_dir_sep in
diff --git a/src/parser/file_key.ml b/src/parser/file_key.ml
index ccf9d193ad1..318cac1bd18 100644
--- a/src/parser/file_key.ml
+++ b/src/parser/file_key.ml
@@ -272,12 +272,15 @@ let relative_path_from ?(dir_sep = Filename.dir_sep) root path =
    compute a relative path from the root — this ensures all suffixes are
    portable relative paths, which is critical for saved state portability
    across machines with different root paths.
-   If the root has not been set yet, returns the path unchanged. *)
+   If the root has not been set yet, returns the path unchanged.
+   The result always uses '/' separators for cross-platform consistency
+   (saved state generated on Linux must work on Windows and vice versa). *)
 let strip_project_root path =
   match !project_root with
   | Some root ->
     if String.starts_with ~prefix:root path then
-      String.sub path (String.length root) (String.length path - String.length root)
+      normalize_dir_sep
+        (String.sub path (String.length root) (String.length path - String.length root))
     else if not (Filename.is_relative path) then
       relative_path_from root path
     else
@@ -296,7 +299,7 @@ let resource_file_of_absolute path = ResourceFile (strip_project_root path)
 let lib_file_of_absolute path =
   match !flowlib_root with
   | Some fl when String.length fl > 0 && String.starts_with ~prefix:fl path ->
-    LibFile (flowlib_marker ^ strip_prefix fl path)
+    LibFile (flowlib_marker ^ normalize_dir_sep (strip_prefix fl path))
   | _ -> LibFile (strip_project_root path)
 
 module For_tests = struct
diff --git a/src/parsing/parsing_service_js.ml b/src/parsing/parsing_service_js.ml
index f412295d6d3..7d92d045984 100644
--- a/src/parsing/parsing_service_js.ml
+++ b/src/parsing/parsing_service_js.ml
@@ -581,4 +581,12 @@ let ensure_parsed ~reader options workers files =
       workers
       next
   in
+  let not_found =
+    if Sys.win32 then
+      FilenameSet.filter
+        (fun f -> String.length (File_key.to_string f) < 248)
+        not_found
+    else
+      not_found
+  in
   Lwt.return (FilenameSet.union changed not_found)
diff --git a/src/services/module/module_js.ml b/src/services/module/module_js.ml
index 5a962cbd843..60bc0216de2 100644
--- a/src/services/module/module_js.ml
+++ b/src/services/module/module_js.ml
@@ -581,7 +581,9 @@ module Node = struct
         let applicable =
           Base.Option.value_map
             applicable_dirname_opt
-            ~f:(fun prefix -> Files.is_prefix prefix (File_key.suffix importing_file))
+            ~f:(fun prefix ->
+              let suffix = File_key.suffix importing_file in
+              suffix = prefix || String.starts_with ~prefix:(prefix ^ "/") suffix)
             ~default:true
         in
         if applicable then