What flattening actually merges
A PDF can carry content that sits above the page rather than in it: form fields you can type into, annotations, comments, highlights, stamps and signature appearances. These are separate objects, and their contents are stored independently of the page they appear on.
Flattening merges them down so that what you see becomes what the page is. A filled form field stops being an editable field and becomes ordinary page content showing the value. An annotation stops being a note attached to a location and becomes part of the artwork. The visual result is identical; the structure underneath is not.
That change is the point. A flattened document renders the same way everywhere, because there is nothing left for a reader to interpret differently — and nothing left for a recipient to edit.
When you should flatten before sending
Flatten a form once you have filled it in. An unflattened form is still editable, which means the recipient can change what you entered, and different PDF readers render form fields with different fonts and alignment — so the document you carefully filled in may not look the way you saw it. Flattening removes both problems at once.
Flatten before printing when a document has annotations you want on paper, since some readers print the page without them by default. Flatten before archiving, because form and annotation behaviour is exactly the sort of thing that degrades as software versions move on.
Do not flatten when the form is a draft somebody else still needs to complete, or when annotations are the point of the document — a manuscript full of review comments loses its function if the comments become part of the page.
Flattening is irreversible, so keep the source
There is no unflatten operation. Once a form field's value has become page content, the field is gone and the value cannot be read back out programmatically or edited without proper PDF editing tools. If you flatten a filled form and then discover a typo, you are correcting it on the original and flattening again.
So the workflow is always: keep the blank form, keep the filled but unflattened version, and treat the flattened file as the outgoing copy. That costs almost nothing in disk space and saves the occasional wasted afternoon.
This matters more than it sounds for anything submitted repeatedly — annual filings, recurring applications, standard contracts. Next year's version starts from this year's unflattened file, and if you kept only the flattened one you start from scratch.
Flattening, file size and long-term readability
Flattening usually reduces file size, sometimes substantially. Form fields, annotations and their appearance streams all carry structural overhead, and a heavily annotated document can shed a noticeable fraction of its size when that structure is merged into the page. On a long review document carrying hundreds of comments, the saving can be large enough to bring an unsendable attachment back under a mail server limit.
The bigger long-term benefit is predictability. Interactive features are exactly the part of the PDF specification where readers differ most, and a document that depends on them is a document whose appearance depends on software you do not control. Flattened pages render the same in a browser, a phone, a ten-year-old desktop reader and a printer.
This is why archival standards lean towards flattened documents. If a file needs to be readable and unambiguous in five or ten years, removing everything that requires interpretation is the single most effective thing you can do to it. The PDF/A family of standards formalises exactly this idea, restricting the specification to features that can be relied on to render identically far into the future.