I didn't simply go outside and sun myself every time I had a one hour wait during a protocol. I worked on something else. When you switch from one project to another you need to continue to record your activities chronologically. Done properly, it won't be confusing at all. You simply read each passage and follow the continuation notes to follow a single project from start to finish.
Magazines do that all the time, to get around ads and to continue long articles.
Just be consistent with the titles of your projects. When you add notes later or correct a mistake, always initial and date your comment. Indicate clearly that this is an additional comment, such as by using a different color ink. If you follow a previously recorded procedure exactly, you need not rewrite the entire protocol. As with projects, be consistent with the names of protocols, formulas, etc.