After using the automatic upgrade to 2.3 I'm getting over 17,000 "files listed below have contents different from those originally downloaded"

From the health check status report:

Check completed on 17,761 files. The files listed below have contents different from those originally downloaded.

If you have edited these files yourself, you may ignore this message, otherwise you should investigate further as this may be evidence of corrupted or altered files.
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Any ideas where to start?

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