It is possbile set/reset the AUTO_INCREMENT value of a MySQL table via
ALTER TABLE some_table AUTO_INCREMENT = 1000
However I need
Assuming that you must fix this by amending the auto-increment column rather than the foreign keys in the table decomposing the N:M relationship, and that you can predict what the right values are, try using a temporary table where the relevant column is not auto-increment, then map this back in place of the original table and change the column type to auto-increment afterwards, or truncate the original table and load the data from the temp table.