Short answer: choose the paper size, choose Fit or Fill, and download. Fit never cuts content; Fill covers the page and crops the overhang. Pages are scaled as vector objects, so text stays sharp and images are not re-compressed.
Why a PDF can look A4 but fail an A4 check
A portal checks the page box, not the paper you print on. A document scanned on Letter paper is 612 × 792 points; a form that expects 595 × 842 points rejects it even though the difference is a few millimetres. Resizing rewrites the box so the file matches the requirement, and the content is drawn into it proportionally.
Mixed page sizes in one file
Scans assembled from a phone, a flatbed and an email attachment often carry three different page sizes. With orientation on Automatic, each page keeps its own shape and only the paper changes — a wide chart stays wide instead of being forced into portrait and shrunk to half width.