If a payment can not be seen on a customer’s account, it could be caused by the AR_Deposit_Check not linking to a valid AR_Deposit_Batch entry. Once you have a valid entry you can use the script below to update the proper ID.
Update C
set Deposit_Batch_Id = ''--Deposit_batch_id from valid entry
from AR_Deposit_Check C
where Deposit_Check_Id = ''--Deposit_check_id that needs to be linked