when i used to do scaffolding we did a number of jobs like this where we had to put temp handrails in front of each skylight and cover them with scaffold boards (sometimes even having to put the handrail around the whole skylight) for people that were working on similar conditions that you face although they would be there for months and not a day or two even having to put handrails round the edges if needed, this was in the early 90s when health n safety was not as big an issue as it is today, you could put a barrier around them but it doesn't stop someone falling through so really they need boards putting on top of them to reduce that risk, but as has already been said a bit of common sence and dont rush the job and there really isn't a problem.