Does Checkout replace the LMA? Will the LMA still control license status or are licenses active for any purchase made through Checkout?

Checkout does not replace the LMA. Checkout works with the LMA to control whether an app is active or inactive, as well as how many licenses an organization has. Checkout automatically creates and updates license records in the LMA, as necessary. You cannot directly edit the license records created by Checkout. To change any of these records, first update the corresponding subscription information in Recurly. Checkout will then automatically update the records in the LMA