Sync notations and free lines on pad to the original document

I love the new version and the ability to highlight!  Much appreciated.  However, sometimes when I go back into an attachment I recently annotated, either just minutes before, or hours, or days before, all annotations get deleted.  Gone.  Hours of work!  Very frustrating.  Today it just happened again, only this time, for the first time ever, I watch them disappear.  Meaning, I opened an attachment, so the color highlight for a fraction of a second, and they were gone.  Scroll to the next page, see the mark ups, and watch them flash out of existance.  Can’t get them back.  Any idea what’s going on?  This has been happening for about one year, even when I used the older version of the iPad app.  I try to prevent it by closing out of a file after marking up so many pages, syncronyzing, and going back in.  If the annotations are still there, great I keep going.  When they’re gone, at least I only lost a few pages to redo instead of the entire 35 page journal article.  Please help!