Changing storage engine to InnoDb from MyIsam is dropping records from table
Are you are using SHOW TABLE STATUS to determine that there is a loss?  Don't trust it.  The "Rows" is an estimate in the case of InnoDB.  Use SELECT COUNT(*) FROM tbl to get the exact row count.

More tips on the conversion:  http://mysql.rjweb.org/doc.php/myisam2innodb