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If there is a LED directly connected to lower MIO Bank of the Zynq then this LED is also always controllable, as this Bank has to be powered for the device to boot. This LED can also be controlled if the PL portion of the Zynq is not configured or even un-powered.

VIO LED

This is an option that is always available as long as we have JTAG Connection to the PL.

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Example of VIO LED, the SoM being used is Kintex UltraScale TE0841, the LED is implemented in F32C Softcore Bootloader that is waiting for Arduino IDE to download a sketch. There is no limit for the number of virtual LED's. It is also possible to attach those VIO LED's to Zynq GPIO when using EMIO mulitplexing, so the same GUI would show LED's controlled by Zynq PS during boot or running Linux. 

LED's on TE SoM's and Baseboards

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