You would have wondered if i’s possible to reconfigure the PL part without any interruption while PS is running Linux. Well, i’s possible and as simple as,

echo '0' > /sys/devices/soc0/amba/f8007000.devcfg/is_partial_bitstream
#echo '1' for partial bitstreams
cat whatever_the_bit_file_name_is.bit > /dev/xdevcfg

Yeah, tha’s it! Make sure you’re running it as root.

Don’t have a nice Linux running on ZedBoard yet? have a look at PYNQ Linux on ZedBoard