Hi Phil, what version of ArcPad are you using? That functionality was built into ArcPad 10. When you use the data manager the photo page has two settings, the path for the photos when features are checked in and a check box for keeping the original paths in your data.
This was implemented as we knew people would want the hyperlink altered correctly on CHeck In, rather than running the "Calculate Field" but they still want the links to be correctly maintained in the field data too so they can still be used while working.