GoodNotes lags and shows blank squares on the page when swiping between pages.
One of the cause is the current limitation of the highlighter tool. Since GoodNotes stores everything in vector format to achieve the highest quality, it needs to redraw each stroke one by one each time a page is loaded. With normal pen, this is not a problem because they are opaque, but with highlighter, semi-transparency requires a lot of processing power. Therefore, it is recommended to avoid too much overlapping highlighter strokes, which usually happens when highlighting back and forth over the same place.
The other cause is content overload. Generally speaking, number of files doesn't affect the GoodNotes performance. But, if a page have lots of graphics or notes, it would take longer time to load. You could however, manage each page with less content to avoid this issue.