You can't change how the links are created by PDFMaker, sorry.
If you've only made a minor change (so the page numbers and positions of the links are generally the same as they were) you can use the Replace Pages option in Acrobat's page thumbnail panel - this will replace the content of each page with those from a new file, but will retain any links, comments or form fields from the original PDF. You may have to tidy up a few, but it'll be less work than replotting them all.
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.