When people talk about "breaking the document flow" they're generally talking about creating paragraph breaks where there shouldn't be, or other abuses of (La)TeX commands such as
~, several of which are listed in the answers to What are the most common mistakes that beginners of (La)TeX and Friends make? and elsewhere on this site.
As long as there is really meant to be a paragraph break at the place you're thinking of inserting this space, you don't need to worry about this "breaking flow", because
- the flow-like concept of hyphenation by paragraphs will not be adversely affected, because you were going to start a new paragraph anyway;
- a new paragraph is a logical break in the flow of reading, so additional space will not greatly upset the reader's sensibilities; and
- as long as the extra space/whatever is used consistently, the reader can recognize its usage and it can then become a reading aid.
The decision of if this extra break/stuff is a good thing or not is a matter of document style/taste, and is up to each individual document designer. In typesetting novels, these are generally known as "scene breaks" and are commonly used to signal context changes within a single chapter. To that end, if you do decide this is a good thing for your design, create it as a macro with some semantically significant name and ensure that it's used consistently, for example:
They left the cafeteria and proceeded to fourth-hour Biology with Mrs.~Duckworth.
\sceneskip % or \scenebreak or \fancyskip or whatever other meaningful name you come up with
Back at Jane's house, a brace of ducks were feeding on the lawn.
This also makes it really easy to change the design: you only need to change the definition of this macro and the whole document will automatically update and remain consistent.
The only other thing to watch out for is how any vertical space is inserted. Because a new paragraph can (and often does) coincide with a page break, when defining
\sceneskip as another form of the
\vspace should be used instead of
\vspace*, so that the extra space is discarded if it comes at the top of a new page.
\sceneskip command is to have spacing and some sort of ornamentation (
* * * or similar), judicious use of the two vertical space commands and
\nobreak is required to ensure consistency of the typesetting. For example, should the ornaments fall on bottom of the page just ended or at the top of the page just begun? Whichever is selected, care must be taken so that the same thing happens at each page break coinciding with the scene break.