Devices and methods for partially upgrading a programmable pluggable transceiver that is in service using the regular datapaths without degrading the basic transparent, hitless pass-through functionality of the transceiver. The programmable logic gate array can be divided into four generalized parts: core logic for basic transceiver pass-through functionality over the datapaths, upgradeable internal logic, connectivity logic for selectively outputting on the datapaths from the core and internal logics, and control logic for isolating, upgrading and reconnecting the internal logic without affecting the basic transparent hitless pass-through functionality of the transceiver.