Strange heavy memory loss (storage) when saving pdf dokument in Preview

This is already taking all of my day and I still havent got closer to a solution, so I really need some help!!
I am currently editing lots of pdfs and other files for notes.
There is one particular big file, ca. 300 MB (part of a book). When I edit this file in Preview (underlining etc.) and save my changes, I loose almost the whole size of the file in disk space (almost regardless of how much I change).
Saving 10 times, that equals ca. 3 GB. Since I am a diligent "back-upper", I loose ca. 3 GB every 90 minutes.
Over the last 3 days, this has consumed more or less 40 GB of my storage space.
I have restarted several times and had to delete a lot of files; the sleepimage file is ca. 1 GB big only, so that is not the problem;
so I have used "Disk Utility" to localize the massive space use.
But here comes the part that made me come here:
Disk utility registers the storage loss in total numbers (35 GB free, next time only 32 GB free), but not within the folders (the single sizes of the folders -Application; Library; User etc-), their sizes stay the same!
I looked through all the forums but I cant figure out what happened to my disk space.
I need some help, cause I need to restore those 40 GB they are being used by something completetly useless somewhere.
Thank you for your time!

In an application that supports Auto Save and Versions, open a document and select
          File ▹ Revert to... ▹ Browse All Versions...
from the menu bar. A browser view of the saved versions will open, with the current one on the left and the saved versions stacked on the right.
To delete a saved version, select it, then move the cursor to the top of the display. The menu bar will appear. Select
          File ▹ Revert to... ▹ Delete This Version...
and confirm when prompted. Click Done to exit the version browser.

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