The issue was that flush_tables() didn't take a MDL lock on cached
TABLE_SHARE before calling open_table() to do a HA_EXTRA_FLUSH call.
Most engines seams to have no issue with it, but apparantly this conflicts
with InnoDB in 10.6 when using TRUNCATE

Fixed by taking a MDL lock before trying to open the table in
flush_tables().

There is no test case as it hard to repeat the scheduling that causes
the error. I did run the test case in MDEV-28897 to verify
that the bug is fixed.