How do you prevent cross-references (made in InDesign) from losing their links in their resulting PDFs when the PDFs are moved (i.e., posted on the web)?
I suppose you refer to cross-references to other documents or external files, because everything inside the document will still work. You cannot prevent it. It is like a link to a file or folder on your HDD or in a network.
As soon as the file or folder is changed (moved, renamed), the link is broken and useless.