You don't seem to be using Create PDF Online... I suggest the Acrobat forum, good luck.
I moved this over to our Acrobat forum. Which Acrobat are you using? Is it Pro or Standard?
Please give more details about your OS...
You might consider just creating a new PDF with the print option (assuming the changes are not major). Then open the old PDF (recommend trying with a copy) and using Insert Pages to insert the new PDF. The links and other markup should remain and only the document should be replaced.
The same discussion apparently in a different forum (before it got moved?) suggests the following:
You can add a script to the main PDF such as:
app.openInPlace = true; //Opens cross-document links in the same window.
app.openInPlace = false; //Opens cross-document links in separate windows.
Advanced > Document processing and the form tools.