diff --git a/configure.ac b/configure.ac
index f0c4d8b5b..b5c165527 100644
--- a/configure.ac
+++ b/configure.ac
@@ -525,6 +525,7 @@ AC_CHECK_FUNCS( wcsdup wcsndup wcslen wcscasecmp wcsncasecmp fwprintf )
 AC_CHECK_FUNCS( futimes wcwidth wcswidth wcstok fputwc fgetwc )
 AC_CHECK_FUNCS( wcstol wcslcat wcslcpy lrand48_r killpg mkostemp )
 AC_CHECK_FUNCS( backtrace backtrace_symbols sysconf getifaddrs )
+AC_CHECK_FUNCS( futimens clock_gettime )
 
 if test x$local_gettext != xno; then
   AC_CHECK_FUNCS( gettext dcgettext )
diff --git a/src/env_universal_common.cpp b/src/env_universal_common.cpp
index dabac1fab..45333a715 100644
--- a/src/env_universal_common.cpp
+++ b/src/env_universal_common.cpp
@@ -808,6 +808,7 @@ bool env_universal_t::sync(callback_data_list_t *callbacks)
     if (modified.empty())
     {
         this->load_from_path(vars_path, callbacks);
+        UNIVERSAL_LOG("No modifications");
         return false;
     }
     
@@ -823,6 +824,7 @@ bool env_universal_t::sync(callback_data_list_t *callbacks)
     if (success)
     {
         success = this->open_and_acquire_lock(vars_path, &vars_fd);
+        if (! success) UNIVERSAL_LOG("open_and_acquire_lock() failed");
     }
 
     /* Read from it */
@@ -831,11 +833,13 @@ bool env_universal_t::sync(callback_data_list_t *callbacks)
         assert(vars_fd >= 0);
         this->load_from_fd(vars_fd, callbacks);
     }
+    
 
     /* Open adjacent temporary file */
     if (success)
     {
         success = this->open_temporary_file(directory, &private_file_path, &private_fd);
+        if (! success) UNIVERSAL_LOG("open_temporary_file() failed");
     }
     
     /* Write to it */
@@ -843,6 +847,7 @@ bool env_universal_t::sync(callback_data_list_t *callbacks)
     {
         assert(private_fd >= 0);
         success = this->write_to_fd(private_fd, private_file_path);
+        if (! success) UNIVERSAL_LOG("write_to_fd() failed");
     }
     
     if (success)
@@ -854,9 +859,26 @@ bool env_universal_t::sync(callback_data_list_t *callbacks)
             fchown(private_fd, sbuf.st_uid, sbuf.st_gid);
             fchmod(private_fd, sbuf.st_mode);
         }
-
+        
+        /* Linux by default stores the mtime with low precision, low enough that updates that occur in quick succession may
+           result in the same mtime (even the nanoseconds field). So manually set the mtime of the new file to a high-precision
+           clock. Note that this is only necessary because Linux aggressively reuses inodes, causing the ABA problem; on other
+           platforms we tend to notice the file has changed due to a different inode (or file size!)
+         
+           It's probably worth finding a simpler solution to this. The tests ran into this, but it's unlikely to affect users.
+         */
+#if HAVE_CLOCK_GETTIME && HAVE_FUTIMENS
+        struct timespec times[2] = {};
+        times[0].tv_nsec = UTIME_OMIT; // don't change ctime
+        if (0 == clock_gettime(CLOCK_REALTIME, &times[1]))
+        {
+            futimens(private_fd, times);
+        }
+#endif
+    
         /* Apply new file */
         success = this->move_new_vars_file_into_place(private_file_path, vars_path);
+        if (! success) UNIVERSAL_LOG("move_new_vars_file_into_place() failed");
     }
     
     if (success)
diff --git a/src/env_universal_common.h b/src/env_universal_common.h
index 203f952b6..3428c6937 100644
--- a/src/env_universal_common.h
+++ b/src/env_universal_common.h
@@ -168,7 +168,7 @@ public:
 };
 
 bool universal_log_enabled();
-#define UNIVERSAL_LOG(x) if (universal_log_enabled()) fprintf(stderr, "UNIVERSAL LOG: %s\n", x)
+#define UNIVERSAL_LOG(x) do { if (universal_log_enabled()) fprintf(stderr, "UNIVERSAL LOG: %s\n", x); } while (0)
 
 /* Environment variable for requesting a particular universal notifier. See fetch_default_strategy_from_environment for names. */
 #define UNIVERSAL_NOTIFIER_ENV_NAME "fish_universal_notifier"
diff --git a/src/fish_tests.cpp b/src/fish_tests.cpp
index cef1857f9..41a0a90fb 100644
--- a/src/fish_tests.cpp
+++ b/src/fish_tests.cpp
@@ -2563,7 +2563,7 @@ static int test_universal_helper(int *x)
         bool synced = uvars.sync(NULL);
         if (! synced)
         {
-            err(L"Failed to sync universal variables");
+            err(L"Failed to sync universal variables after modification");
         }
         fputc('.', stderr);
     }
@@ -2573,7 +2573,7 @@ static int test_universal_helper(int *x)
     bool synced = uvars.sync(NULL);
     if (! synced)
     {
-        err(L"Failed to sync universal variables");
+        err(L"Failed to sync universal variables after deletion");
     }
     fputc('.', stderr);
 
diff --git a/src/wutil.cpp b/src/wutil.cpp
index 0e233ac78..a3a51dac7 100644
--- a/src/wutil.cpp
+++ b/src/wutil.cpp
@@ -545,15 +545,20 @@ file_id_t file_id_t::file_id_from_stat(const struct stat *buf)
     result.inode = buf->st_ino;
     result.size = buf->st_size;
     result.change_seconds = buf->st_ctime;
+    result.mod_seconds = buf->st_mtime;
     
 #if STAT_HAVE_NSEC
     result.change_nanoseconds = buf->st_ctime_nsec;
+    result.mod_nanoseconds = buf->st_mtime_nsec;
 #elif defined(__APPLE__)
     result.change_nanoseconds = buf->st_ctimespec.tv_nsec;
+    result.mod_nanoseconds = buf->st_mtimespec.tv_nsec;
 #elif defined(_BSD_SOURCE) || defined(_SVID_SOURCE) || defined(_XOPEN_SOURCE)
     result.change_nanoseconds = buf->st_ctim.tv_nsec;
+    result.mod_nanoseconds = buf->st_mtim.tv_nsec;
 #else
     result.change_nanoseconds = 0;
+    result.mod_nanoseconds = 0;
 #endif
 
 #if defined(__APPLE__) || defined(__DragonFly__) || defined(__FreeBSD__) ||  defined(__OpenBSD__) || defined(__NetBSD__)
@@ -590,12 +595,7 @@ file_id_t file_id_for_path(const wcstring &path)
 
 bool file_id_t::operator==(const file_id_t &rhs) const
 {
-    return device == rhs.device &&
-           inode == rhs.inode &&
-           size == rhs.size &&
-           change_seconds == rhs.change_seconds &&
-           change_nanoseconds == rhs.change_nanoseconds &&
-           generation == rhs.generation;
+    return this->compare_file_id(rhs) == 0;
 }
 
 bool file_id_t::operator!=(const file_id_t &rhs) const
@@ -617,7 +617,7 @@ int compare(T a, T b)
     return 0;
 }
 
-bool file_id_t::operator<(const file_id_t &rhs) const
+int file_id_t::compare_file_id(const file_id_t &rhs) const
 {
     /* Compare each field, stopping when we get to a non-equal field */
     int ret = 0;
@@ -627,5 +627,13 @@ bool file_id_t::operator<(const file_id_t &rhs) const
     if (! ret) ret = compare(generation, rhs.generation);
     if (! ret) ret = compare(change_seconds, rhs.change_seconds);
     if (! ret) ret = compare(change_nanoseconds, rhs.change_nanoseconds);
-    return ret < 0;
+    if (! ret) ret = compare(mod_seconds, rhs.mod_seconds);
+    if (! ret) ret = compare(mod_nanoseconds, rhs.mod_nanoseconds);
+    return ret;
+}
+
+
+bool file_id_t::operator<(const file_id_t &rhs) const
+{
+    return this->compare_file_id(rhs) < 0;
 }
diff --git a/src/wutil.h b/src/wutil.h
index 5c9a0ec2c..9897439a0 100644
--- a/src/wutil.h
+++ b/src/wutil.h
@@ -143,6 +143,8 @@ struct file_id_t
     uint64_t size;
     time_t change_seconds;
     long change_nanoseconds;
+    time_t mod_seconds;
+    long mod_nanoseconds;
     uint32_t generation;
     
     bool operator==(const file_id_t &rhs) const;
@@ -152,6 +154,9 @@ struct file_id_t
     bool operator<(const file_id_t &rhs) const;
     
     static file_id_t file_id_from_stat(const struct stat *buf);
+    
+    private:
+    int compare_file_id(const file_id_t &rhs) const;
 };
 
 file_id_t file_id_for_fd(int fd);