I think you’re making it more complicated than it needs to be.

Correct me if I’m wrong, but it sounds like you have created a separate .indd file for every recipe and then placed a single-page .indd file at the beginning of each “section” as you’re calling it. What you should have is an InDesign book file with an .indd file for every “section” that is multiple pages long and includes every recipe for that section flowing throughout the file.

For example:

My Great Recipe Book.indb — this is your book file
TOC.indd — this will be a separate .indd file where your Table of Contents and any acknowledgments or preface materials will be included
01_Breakfast.indd — this would have a title page introducing this section, followed by your Eggs Benedict, French Toast, etc. recipes
02_Appetizers.indd — this would have a title page introducing this section, followed by your appetizer recipes, etc.
03_Dinner.indd
04_Dessert.indd
…

You will easily be able to create your TOC after all of the other chapters (which is a more accurate term than “sections” in InDesign, since “section” is a different feature) are completed, as long as you use a consistent paragraph style at the beginning of each chapter to name your chapter, such as “Chapter Title.” You can do a more in-depth TOC if you also use consistent paragraph styles for the names of all of the recipes as well.

If you want to add further sections between recipes, say you want categories within “Breakfast” for “Eggs” and “Muffins”, you can use another paragraph style to define those and add that line before the first recipe in that category. The section feature doesn’t really import into the TOC, just paragraph styles, so you’ll want to utilize those to define your sections. Section markers are better suited for other things.

I hope this makes sense!