What are these %% begin id-pn2xitti%% and %% end id-pn2xitti %% and ^pn2xitti?
These are the persistance-markers of the indivual highlights, and the reference-id to that highlight.
The markers are meant for the importer. It will skip all text within those markers, so they stay when updating a zotero-import. Removing a marked block does not work well, it will not be reimported. Don't know how to fix that. If you want to reimport a highlight-block, best is to change the highlight in zotero (for example change the color). This will update the id, and on the next import the new highlight will be imported.
The reference-id is used like this: [[@name-of-the-note#^pn2xitti]]