Thanks for reporting that. Fixed in Emacs master via the attached.

For the more general issue I'm planning to add a builtin boolean variable current-time-list soon, that is t for (HIGH LOW MICROSEC PICOSEC) format, nil for (TICKS . HZ) format.
From 3abb3681b57d7c8ca7fa808addb0a10b6b109cab Mon Sep 17 00:00:00 2001
From: Paul Eggert <egg...@cs.ucla.edu>
Date: Wed, 27 Apr 2022 00:29:26 -0700
Subject: [PATCH] Use org-time-convert-to-integer instead of by hand
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* lisp/org/org-macs.el (org-file-newer-than-p):
Don’t assume list-format timestamps, by using
org-time-convert-to-integer instead of doing it by hand.
---
 lisp/org/org-macs.el | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lisp/org/org-macs.el b/lisp/org/org-macs.el
index b10725bd52..92591b5bb7 100644
--- a/lisp/org/org-macs.el
+++ b/lisp/org/org-macs.el
@@ -257,15 +257,16 @@ org-fit-window-to-buffer
 
 (defun org-file-newer-than-p (file time)
   "Non-nil if FILE is newer than TIME.
-FILE is a filename, as a string, TIME is a list of integers, as
+FILE is a filename, as a string, TIME is a Lisp time value, as
 returned by, e.g., `current-time'."
   (and (file-exists-p file)
        ;; Only compare times up to whole seconds as some file-systems
        ;; (e.g. HFS+) do not retain any finer granularity.  As
        ;; a consequence, make sure we return non-nil when the two
        ;; times are equal.
-       (not (time-less-p (cl-subseq (nth 5 (file-attributes file)) 0 2)
-			 (cl-subseq time 0 2)))))
+       (not (time-less-p (org-time-convert-to-integer
+			  (nth 5 (file-attributes file)))
+			 (org-time-convert-to-integer time)))))
 
 (defun org-compile-file (source process ext &optional err-msg log-buf spec)
   "Compile a SOURCE file using PROCESS.
-- 
2.32.0

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