TransFR (Transparent Field Reconfiguration) is a technology that helps minimize system interruption. This is supported through JTAG and Non-JTAG port (example Wishbone). However, there are some disadvantages of Non-JTAG TransFR. It does not allow user to release I/Os at a specific time during TransFR. It does not allow user to customized I/O value during TransFR. I/O values are kept as is.

For further information, you may refer to Minimizing System Interruption During Configuration Using TransFR. The document can be downloaded at the Lattice website.