JTAG instructions should not be applied if a non-JTAG configuration process has already begun.
This is because configuration should not be interrupted and the I/O states are undefined.
It is recommended that if JTAG configuration is to be used, the Mode pins should be set to select JTAG Mode to prevent access through any other configuration modes.
Alternatively, hold off configuration, or wait until non-JTAG configuration completes before reconfiguring via JTAG instructions, which have priority over the Mode pin settings.
Configuration instructions such as CFG_OUT, CFG_IN, JPROGRAM, JSTART, and JSHUTDOWN, and boundary scan instructions such as SAMPLE/PRELOAD and EXTEST, should be avoided during non-JTAG configuration.
Note: USER instructions are not available until the completion of configuration.
See the Configuration User Guide for the relevant family for more information.