You can specify several processing options that apply to all cross references:
[HTMLOptions]
; RemoveFilePaths = Yes (default, strip hyperlink and xref paths)
; or No
RemoveFilePaths=No
; ListMissingRefs = No (default)
; or Yes (identify missing xrefs to stderr)
ListMissingRefs=No
; CheckAllRefs = Yes (default, even if they seem unchanged)
; or No
CheckAllRefs=Yes