Unfortunately, you cannot alter the check sum and count total once a batch is opened, except when you delete a successfully scanned check from a batch. If you cannot scan a check (too wrinkled, and jams for example), then you will have to delete this batch and start a new batch without that check.
To alleviate this, scan all the checks in the batch before entering any Lease ID information. You could also try to scan the wrinkled checks first. If any checks do not scan, set them aside, delete the batch, and start a new one with a lower check count and total.
The control count and total is important to the check scanning automation. The only way it can be altered after you start a batch is to delete a successfully scanned check, and choose to lower the count and amount when you do so.