Flattening a PDF is the process of converting all of the PDF’s layers to one single layer, which will allow you to edit and save it in a much smaller file size.
The only implication is that this process will make text and images in the document inaccessible.
With PDF flattening, the exact way the PDF looks like will be turned into an image, so that it looks the exact same.
However, it will not be editable anymore in any way.
Same looks, no more functionality.