Check removed/dropped from Payment batch?

User originally ran the batch closure report for batch CHECK-AAA-4045096.  At that time, Check number 2465 for cust 5381066 in the amount of $16,225 was reversed as a held check and included in the batch for deposit.   User needed to then go in and make adjustments so ran the batch closure program again for this same batch.  However, when she did that, the report generated and NO LONGER SHOWED CHECK #2465.  The check dropped out of the batch.     When looking at the actual receipt, the check does NOT show the batch name in the screen header where it normally appeared.