How much would it cost to cut and patch a 3' x 3' hole on a roof of an organization building to fit HVAC equipment?
IT depends on what material the roof is made of.
Some materials are cheaper and easier to repair then others.
Not sure what nature of office building you are talking roughly speaking. My suggestion is get a professional company to do the work. Be sure they will warranty their work. Presently I am having warranty work done on the roof I cart care of. If it wasn't for the warranty I would be asking for a a lot of money to repair what be installation deficiencies from 8 years ago.
You are going to have to price this out yourself. A foremost part of an Engineers job is determining the cost of projects. I can't let somebody know you from the computer monitor because I have to see the location the unit will be installed.