Uncommitted changes, when both versions come from git. Commit first, or the working tree is ignored. To compare the working tree with another copy on disk, use --from-path.
Properties that the text does not show. The properties block is not part of the PDF, so a change of status: draft to status: approved is invisible unless a Meta Bind field or a Dataview table shows it. See Properties and Meta Bind.
Moves of short or rewritten text. A paragraph counts as moved when it has at least six words and is nearly the same in both places; a list item when it is unchanged and stays in the same list. Other text is shown as removed at the old place and inserted at the new one. See Moved text.
Notes outside ROOT, unless they are embedded or queried. A change in an embedded note or in a note a Dataview query reads does show up, since the embed and the query run before the comparison.
Layout. Template changes, page breaks and landscape pages are not compared. Wide tables and figures stay on portrait pages in a blackline redline.
Changes inside a diagram. A changed Mermaid diagram is shown as the old and the new drawing, not with marks inside the drawing.
Keep one sentence per paragraph change. The comparison works per block, so a small edit in a long paragraph is shown word by word, while a rewrite of the whole paragraph is shown as removed and inserted.
Separate unrelated edits by an unchanged paragraph or list item where you can. Each group of neighbouring changes gets one bar in the margin and one line in the summary.
Reflowing text and re-padding tables is fine: line breaks and spaces inside a paragraph and the padding of table cells are not changes. With hard line breaks (the default) a moved line break still moves the break in the PDF.
Avoid ~~strikethrough~~ in controlled documents. It renders as del, the same element as removed text, and looks like a removal in the redline.
Use tags for releases (v1.0.0, v1.1.0). Then a redline of any two releases is one command, and the CI recipes in Usage work without changes.
For a pull request, compare against the merge base, not against the tip of main. See Comparing versions.
Look at the diffed Markdown when a mark looks wrong: --debug keeps redline_assembled.md in the build folder next to the PDF.
A redline of a new folder is one long insertion. Compare from the first commit that has the folder, or make a normal export instead.