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Admin Tools keeps a record of the following properties of each critical file"

• File size, accurate to a byte
• Last modification time, accurate to the second
• MD5 hash of its contents
• SHA-1 hash of its contents

If any of these properties change it will report the file as changed.

It's possible that the last modification time changes without any of the other properties changing if the file is restored from a backup or if it's opened and saved without any changes. This could also happen if your host was doing any kind of maintenance work on their servers which required them to restore files out of a backup of their own.

Since you compared the contents and, I presume, the sizes of the files and found no change I would believe this is what happened.

However, once Admin Tools detects that the file has been modified it stores the new properties of the file in the database. The fact that you keep receiving this email tells me that either the database recored is not being updated or something is changing the file modification time of your files all the time.

Find the #__admintools_storage table in your site's database, where #__ is to be replaced by the table name prefix you use on your site (it's the $prefix value in your site's configuration.php).

Find the record where the key column is set to criticalfiles. Delete it. This re-initialises the critical files feature.

If you keep receiving emails about critical files having changed please check their file modification date every time you receive an email and compare it with the previous one. If it keeps changing something weird is going on with your site; try restoring from a backup. If the problem persists contact your host. The file modification time should only change when the file is being written to and there is no reason for these files to be written to if you're not updating Joomla or its templates.