sminded

I have gsm repeater with a zynq and during boot I can see that it fails to run many commands from the petalinux boot, looks like a corrupt file system. Normally I will reload these devices from the web admin page, but now I need to reflash the qspi flash i guess? I have access to boot and bin files from the petalinux boot folder. Could someone point me in the right direction for an as simple as possible rescue? The board has some ftdi chip as well as ethernet connection. The corrupt file system makes it reboot after a few seconds (20-30 secs)