We have got datafiles folder from the customer, so I have no steps for reproducing this situation. However, let's assume that we want to get out of it somehow.
Please see results of two queries in the attachment. I would like to highlight difference in
Somehow we managed to have column length updated in information_schema.columns (597 bytes length), but not in information_schema.innodb_sys_columns (192 bytes length).
mysql_upgrade reports that mysql.innodb_table_stats as well as mysql.innodb_index_stats are up to date, while customer continue getting
last_update type is also wrong, you can see it the attached file, but it is not that obvious as string length difference.
I've prepared archive of the internals, but it is 75Mb and I cannot attach it here.