Preview.app Very Slow To Save Highlights on PDF (rMBP, OS X 10.10.3) I have scanned a textbook into PDF. The file is 725 pages and 1.73 GB large. It is mostly text but there are a few images per page. Now that the book is scanned in, OCR'd (SearchScan exact), and Bookmarked (all done via Adobe Acrobat Pro XI), I can read the file digitally. I am a big fan of annotating (specifically highlighting) my readings in Preview.

So I open up the file in Preview.app to begin my studies. It scrolls a little slow and lags a bit, but overall I can work with the file given (to be fair, the size is large). However, saving the file after any highlighting is a nightmare.

When I highlight a word, and then hit CMD+S, Preview "saves" the file in less than a second. However if I immediately hit CMD+S a second time (which is the only way to actually save the file, I believe, because only after the second Save does the "Edited" marker at the top of the file go away), I instantly get a spinning beach ball of death. The ball spins for several minutes (15+). After the Save is completed and the "Edited" tag disappears, I "X" out of the file with the red X, and the beach ball process occurs for a second time. It is almost as if Preview is re-saving the entire document, instead of just the one page which I annotated.

I have spent many hours trying to figure out how to fix this. I have encoded and re-encoded the PDF in many different manners. I "Optimized" the PDF in Adobe Acrobat Pro XI using JBIP and then with ZIP. I "Exported" the file out of Preview itself, with the Quartz filter. I reduced the quality of the PDF so that it was only 750 MB large. I repaired disk permissions. None of these various methods significantly decreased the beach ball time of the Preview saving process.

I'm sure I could break up the textbook into smaller files, but this is an inconvenience. I could also use a different app to annotate the PDF but I've always liked Preview up until now and use it consistently for all of my note-taking needs. In fact I have a 300 page textbook PDF that is 150 MB and Preview handles the file well; it only takes maybe 10 seconds to save and the file does not lag.

I can't really decrease the quality (ie size) of the PDF because the text would be hard to read.

I realize it's a large PDF, but I don't think I'm asking too much of Preview for 2015. I would really appreciate help with this matter as this saving issue is putting me behind.

My computer:
MacBook Pro (Retina, 15-inch, Early 2013), 16 GB 1600 MHz DDR3, 2.4 GHz Intel Core i7, NVIDIA GeForce GT 650M 1024 MB, Yosemite 10.10.3

Edit 05/30/15: I think something is wrong with the Preview.app, not my PDF file. I have a scanned textbook PDF (530 pages, 330 MB) that I've reference periodically over the past year and it used to be a lot zippier. Nowadays the book takes about 30 seconds to save. Not a very long time, but longer than I remember...
What I ended up doing was simply break the textbook chapters into individual PDF files. Not the ideal solution, but at least the saving process for highlighting is relatively quick with chapter files.