I had to edit by hand, because etc/zebdradb/xml/koha-indexdefs-to-zebra.xsl does only support "substring" in handle-one-index-control-field template. It is good for MARC21, but not for UNIMARC : in MARC21, indexing substrings is needed for controled field (001-009, with no subfields) But in UNIMARC it is needed for subfields of 1XX fields. So if DOM indexing is working with these new files, we may need to change koha-indexdefs-to-zebra.xsl.
In which patch have you modified koha-indexdefs-to-zebra.xsl file directly? The 'normal' way to modifiy Zebra DOM indexes is a two step process: 1. Edit indexes defintion in biblio-koha-indexes.xml file. 2. Generate Zebra index building XSL file koha-indexdefs-to-zebra.xsl from indexes defintion file biblio-koha-indexdes.xml. If you bypass step 1, it means that index definition XML file is not necessary anymore, and so must be removed/deprecated.