I fix flat roof and replace them as well. Flat roofs are the most problematic roofs because of the misapplication of standard practices ( this means they are easy to cheat on because not all the proper four layers are installed and if they are, then they are installed poorly at times ). Shingled roofs are two layers thick thus half the expense.
NOTE: Due to the lack of ability to insulate under the flat roofs from inside a home without causing lots of drywall damage I find myself putting in lots of insulation under these roofs because when they are open the insulation is easy to install without causing any interior damage. 20% of the flat roofs I do have NO insulation in them!
A flat roof is a roofing structure with less than a nine degree slope in it. The problems with flat roofs is that in our winters there is always one inch of water that sits on the roof and this has one inch of ice on top of it and then a layer of snow to top it all off. This means that the roof has to be built to withstand puddling and hence must be a completely sealed membrane. think in terms of a swimming pool liner. 100% waterproof. This is accomplished on most residential applications with a four layer thick torch welded membrane ( this means you melt pieces together to make a fully waterproof membrane - see the photo above ).
To build a residential and in some cases a commercial flat roof, one tends to remove all the old layers of the old roofs. These layers are sometimes wet inside and trap water in them. This trapped water then turns to steam wrecking the newly installed roof etc... So we almost always remove the old layers. Once any rotten wood is repaired, we install a fireproofing layer made of a fiberglass material, then a torch safe fiberglass board is installed and then we torch weld two layers of a thick rubber membrane ( 'modified bitumen' is the technical term - which means modified tar. It is modified into rolls with polyester layers in it. A picture of it is above ). This makes the four layers. There are other types of flat roofs and most of them suck badly. Commercial roofs are usually 'tar and gravel' as they are cheaper on bigger projects. Skylights on flat roofs are perfectly safe with the only stipulation being that they have to be installed high up off the roof. Higher than any puddling is possible. Usually 6'' is enough. A common mistake is a shingled roof skylight installed into a flat roof. I fix one a week like this. A fancy application is the two nice velux skylights installed above sloped away from any direct sunlight and glass to keep it quiet in a bedroom.
Please note in the photo above the little black lines. This is evidence the roof has been torch welded together ( torch welding means: applying a flame to weld the flat roofing materials together ). The black lines are called 'bleeds' . This means and shows that two pieces of the membrane have been fully sealed and make inspection for waterproofness easy. All you need to see is the black lines to see that the melting of the individual pieces has occurred and thus all pieces have become one and hence fully waterproof.
Flat roofs are where lots of problems occur because the wood is frequently rotten under them and/or they have no insulation in them as noted above and very often too many layers causing the rafter to sag which causes unwanted puddles on the roof. All fixable and sometimes a surprise mid job. Ask me about this if you need further data.