Just to be sure I'm being 100% clear:
Hero Designer has two inputs in the exporting process, right? The data from the character sheet inside Hero Designer (i.e. Powers, Characteristics, Background, etc.) , and the data from the export format (i.e. html tags, other strings in the HDE file, etc.).
It appears that REPLACE only works on the data from the character sheet, while REG_REPLACE applies to both inputs. If that's not the intended behaviour, then I think I found a bug.