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In the commit 3b4b512d8e42bb3d33cf78789754cd10ff310646, Marko made the comment:
To truncate such "contaminated" or "bloated" undo log tablespaces (when using innodb_undo_tablespaces=2 or more) you can execute the following SQL:
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BEGIN;INSERT mysql.innodb_table_stats VALUES('','',DEFAULT,0,0,0);ROLLBACK;
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SET GLOBAL innodb_undo_log_truncate=ON, innodb_fast_shutdown=0;
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SHUTDOWN;
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The first line creates a dummy InnoDB transaction, to ensure that there will be some history to be purged during shutdown and that the undo tablespaces will be truncated.
Sure, its not the full ibdata1 space, but might be what you need.
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