What do you mean by accept all edits. Once the edits are done and saved they are accepted as such. It may be that there is some other thing you mean by edit. There are many aspects of edits that might be done. The typical text or object edits are what I am talking about. When links are changed that is set. So what are you talking about accepting? Please indicate just exactly what you are doing to "edit" your PDF?
It may be that your edit is just markup that is not part of the PDF. In some cases you can flatten the PDF to get them as part of the document.
... but haven't found a way to have my changes incorporated into the document.
There is no way.
What is important to understand is the PDF (described/defined by ISO 32000-1) is not a file format intended to support editing, formatting, or page layout such as is supported by a word processor or page layout application.
So why the Edit Text markups provided by Acrobat?
The markup PDF can be referred to while correcting the authoring file from which the PDF was created.
The markups can be exported to a comment summary report that may be used to facilitate corrections to the authoring file.
The markups can be brought back to a source Word authoring file via PDFMaker's Acrobat Comments feature.
A Framemaker file can be converted to PDF for review/commenting and those markups brought back into the source FM file.
If you simply use the Text Touchup Tool (changed name in AAX), that becomes part of the document. But lack of reflow and such often make such changes very strange and sometimes unusable. Possible minor changes like in spelling can even be a pain. It is just not a roll that Acrobat was designed for as Dave mentioned. The markup is just a form of annotation and does not become a part of the document as you have found.
If your document started it's life as a Word file, you could round-trip the comments back into Word to incorporate the changes. Here is a video tutorial that details how to do this:
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