Multiple manuscripts created in a PDF

I recently used my iPad to annotate a manuscript I was proofreading for a client (300 pages, a novel). It was in Dropbox, I opened it using Adobe Acrobat, and annotated it in several sessions. Today I noticed that the PDF is now over 900 pages long and three versions of the annotated manuscript are in the single PDF one after the other. I can use this, because the comments are clearly listed in the comments list when I transfer the PDF back to my Mac. However, I need to know what I'm doing wrong so this doesn't happen again. Is there something I should be doing while saving and/or closing the PDF I'm annotating?

Sorry - have I posted in the wrong forum? I thought iOS was the operating system used by Mac platforms including iPad. I couldn't see a specific iPad forum so thought this was the closest match, and that someone might be able to offer advice.
(I can see that I've mistakenly typed "Acrobat" in my original post instead of "Reader" so maybe that's caused the confusion? I don't think I can edit that, sorry.)

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