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Originally Posted by Bookworm_Girl

It's possible there may be a lag when highlighting PDFs. There was a discussion in this thread link a few days ago. You might want to check it out and see if it sounds similar to your problem.
https://www.mobileread.com/forums/showthread.php?t=93009

I had not been note-taking while this lag was occurring last night, but some of the description is similar (but I don't think there's any link, really). Having suspected it was an issue with having too many notes on the file in question, I deleted all of them; there was no improvement. I switched to reading PDFs with no notes and still had lag. Then I suspected that I may have too many PDFs, so I deleted many of them, and again no improvement.

Just a few minutes ago, I deleted the remainder of my notes on my reader (only about 20 one-word highlights, not much at all) and no luck.

I find this issue really weird; the PDFs in question are 300 or so pages long, but then problem persists for PDFs of 5-pages, too.