As others have mentioned, Fortify and most scan tools don't just scan the delta of files changed. They scan the entire code base.
With Fortify, it's a resource intensive tool by nature. And if you code base is sizeable, you'll need a strong machine to cut through it quickly. I suggest the following...
Assuming you have access to AWS or Azure, spin up two images. One is a medium-light strength image, which will hold Fortify portal and reporting. This one can stay up 24 hours. Secondly, then spin up another very strong image, which will only be active during scans.
To do this, use Jenkins to make API calls to spin up the scanning machine image just before you start the scan.
If it has good computing power, even with large code bases, it shouldn't take more than a couple hours to scan.
Once the scan is complete, it'll send the results over to the main portal/reporting server and you can again use the API calls to shut that instance down. This is to keep your costs down.
Lastly, we have to talk about Fortify vs. Sonarqube. My personal take is that you should use both. After pouring over results from both, Fortify picks up more vulnerability related items. Sonarqube picks up more syntax/logic related issues, with some vulnerability stuff mixed in.
In my experience, they compliment each other nicely.
Hope that helps, if you have further questions, send me a PM or ask it here.