We took off fencing off a flat roof due to the replacement of the roof
with roll down material
now the fencing needs to be replaced
question is How do we replace fencing without nailing into the new roof ?
Let me guess, there weren't any prints or specs for this job. Right?
The correct way would have been to anchor the pipes rails supporting the fencing before the insulation and membrane was installed, then flash around them.
A second method is to now anchor the pipe bases directly to the roof, screwing through the new membrane into the solid roof deck, then install conical plumbing boot penetration flashings around the pipes and covering the anchoring flanges.