I only do one wash with Nikwax, the waterproofer goes in the rinse programme!
Never had an issue over quite a few years of using it on various makes of gear, including my Roadcrafter!
The only exception was an Oxford suit where the material lost some original coating that caused it to start fraying on the jacket where it touched the velcro on the pockets after only it's first wash. Made it look very bad, a jacket with hairy sleeves!
It went back for a refund as it was only 7 months old!