Convert Cross-Reference Pro Links to Native InDesign Cross-References

Maybe it's possibe to take your InDesign file and do a script to convert DTP Tools's cross-references to InDesign cross-references. DTP Tools's cross-references are scriptable, but you'd have to have the plug-ins installed. I've no idea whether the DTP Tools's cross-references are visible without the plug-ins and if they are, to what extent.

> Since InDesign now has the ability to cross-reference

This is true. But bear in mind that DTP Tools's cross-references have two advantages over InDesign's: they can do cross-references to footnotes and you can suspend their updates for faster processing of book files. 

(I have no connection with DTP Tools.)

I see that Cross-References Pro is a paid product from DTP Tools which is still being sold.

Are you asking someone to use their paid copy to implement the features you need? That doesn't seem ethical. You should acquire the plug-in from DTP Tools yourself.