Include only relevant information from your notes when writing your paper

Keep the structure of the text flexible.
Once you have done all the required research, develop a flexible structure for your paper. A flexible structure will give you freedom regarding what information to include in which chapter and what not to include at all.

Work on multiple manuscripts at a time.
Working on multiple manuscripts requires that you draw upon the information from your collection of notes. As arguments are developed in one manuscript, you may see that some of the resulting ideas can also be used in the other manuscript. In this way, you can include the information and the developed ideas from one paper in another.

Make a separate file that contains all the excluded information.
Keep the information you decide to exclude from your paper in a separate file. This is similar to step two, as you can use this excluded information in some other paper in the future.