System and method for implementing multi-channel operations in a programmable hardware element (PHE). A hardware configuration program, including a processing function, inputs and outputs of the processing function, a plurality of channels, and channel scanning functionality for the plurality of channels, is specified. A PHE is configured with the hardware configuration program, including implementing the processing function and the channel scanning functionality on the PHE. A respective state and configuration of each of the plurality of channels is stored in a memory of the PHE to enable logic-sharing between each of the plurality of channels. The PHE is operated, including performing channel scanning on the plurality of channels, and updating the configuration of one or more of the channels in the memory of the PHE without interrupting the channel scanning, without taking any of the channels offline, and/or without interrupting a continuity of an output of the PHE.