Do you think it’s a good idea to group related fieldsets together using a <section> tag?
Say that there are several fieldsets that hold questions in <legend> tags.
Does this break the format if I group these fieldsets together with <section> tags, labeling them with headings, and does this break the flow for users with assistive technologies?
I think I can see a use case for this which makes sense. I don’t recall ever seeing field sets in the wild, though, so am not sure if it’s actually a pattern people use.
I’m far from an accessibility expert, but… have you tried building it and just seeing what happens when you use assistive technology? To test how easy it is to understand with a screenreader, try moving the browser window to a second monitor with the display turned off, or just cover your screen (with a very soft cloth to you don’t damage it!) and force yourself to rely on the screenreader to move around. Even better: get someone who doesn’t know what you built to try this. The ideal: find people who actually rely on assistive technologies who are willing to help you with testing.
A suggestion for the future: maybe put ‘accessibility’ in the topic title when applicable. Some of us are particularly attracted to such issues, whether we’re trying to learn ourselves or we’re keen to help others. Or both! I give you kudos and a like for caring enough about accessibility to ask for guidance 
Here is a source of information:
Well, if I understand it correctly, is sounds like it´s like a div elemenet, but you should use section if you just simply wrap contents together.
it makes sense, because div can be anything you want, but section probably tell the assistive technology program that the content here are bunched together,so they should be handled that way.
I think the Survey form exam project had the same logic. The basic data (name, email, etc) was one section and the rest (checkboxes, radio-buttons, etc.) was another section.
I just guess: Maybe it also helps with auto-fill too, if every auto-fillable input wraped together in HTML.
So answering your question: If you wrap related questions with their labels together in a section, I think it will help accessibility.