I have this same issue.  Building was sold and the deposits were included in the closing transaction.  The deposits need to be adjusted somehow so I can reconcile the account and terminate the lease.  There is no information on the knowledge base that I can find...

You can create a new Charge Type for the closing transaction so that it has the correct GL account to use (assigned as the Revenue account on the charge type) when closing out the deposit. Then you'll create a charge using this new Charge Type for the amount of the deposit, then in Reconcile Account, apply the deposit to this charge. 

You can create a new Charge Type for the closing transaction so that it has the correct GL account to use (assigned as the Revenue account on the charge type) when closing out the deposit. Then you'll create a charge using this new Charge Type for the amount of the deposit, then in Reconcile Account, apply the deposit to this charge. 

Thanks!!!