I think you have verified the bitstream is working, which is good. I am not quite familiar with that board, but it is possible to just load bitstream as a service (like the boot_leds.service) during OS booting. In that case you don’t have to comment out line 139-141. Also, if your ethernet depends on some IPs in FPGA (e.g. some device tree entries required), you can load the bitstream along with the device tree segment; PYNQ supports that kind of operation. After bistream is loaded, you can try restart your ethernet service / or ifdown + ifup to see if it works.
