First of all, to your question:
Yes, make these emphasized.
Any mission/business-critical concept that appears multiple times in your documentation should generally be unambiguous and well-defined. Part of your goal with documentation is to ensure that readers would over time learn these terms and their meanings, and be able to quickly detect issues in the documentation or the underlying system. Emphasizing a word when it serves as one of these domain nouns helps ensure that readers give it the appropriate consideration.
In the cases that a term can appear both as a domain noun and also as an unrelated natural text, it is advisable to get rid of the unbound name to reduce confusion. If it is not possible to do so, then having a visually clear way of distinguishing between the two is critical, hence emphasizing makes sense. Think about the way modern IDEs distinguish general identifiers from keywords, or how they distinguish variables from members. Visual cues are the among the best ways to disambiguate things.
If you are distributing electronic documentation in addition to printed (I hope you are), then you probably want each instance of the well-defined term to be linked to some glossary. In that case, you would be providing something like a hyperlink or an indication, so you could skip the caps.
Now something more general:
I did my Ph.D. work on how people read API reference documentation (JavaDocs in this case). While this doesn't apply directly to the situation you're describing, some of my general findings might (with no guarantees).
I found that when people choose to read a piece of text, they already have a goal in mind, and they also have a preconceived notion of what that text would say. As a result, they are more likely to miss anything that is not in their expectations, even if it is starting them in the face and sometimes even after repeated readings.
For instance, suppose that I am reading the instructions for "how to charge an electric car". I would come in expecting to see something about turning off the car, plugging it in some way, paying in some way, and waiting a certain amount of time. I will likely be scanning the text for that. If there is a line somewhere like "make sure that the car temperature is below X before proceeding", I would be more likely to miss it because I'm not looking for it.
What I'm trying to say is that your goal as documentation writer is not to cover your bases (legal is for that), but to ensure that someone who is skimming the text (and most people would be skimming) would get the most out of it. This means that your focus should be on emphasizing things that are likely to be unexpected, and any trick in the book is good for that, including caps, words like "warning!", "make sure that", etc.
After you write your documentation, do actual usability testing. Give a coworker (or more than one) who's not familiar with the business process 10-15 seconds to read something like your occurrence paragraph, then ask about the special clauses there. If you see that enough people missed that, consider emphasizing the unexpected.