This is what we've done to get the missing entry items into a state where they can be merged back into the main collection whenever SK finds that one is missing:

1. Generated a rescued.xml file starting from the complete set of unmerged_xml documents, collated using xincluded-complete-list-expanded.xml, and running a new transform called retrieve_lost_from_unmerged.xsl.
2. Manually fixed nested <ENTRY> tags (there were only six instances).
3. Ran rescued.xml through remove_empty_tags_from_rescued.xsl, which removes the initial empty tag that caused all our problems; it also turns any child::infl tag into a comment (SK thinks this will be the simplest way to preserve that information). The output is called rescued_empties_removed.xsl.
4. Ran rescued_empties_removed.xsl through expand_separated_xml.xsl to produce rescued_empties_removed_expanded.xml. In this case, I tweaked the XSLT file to preserve comments from the preceding steps, recording the file of origin of the entry, and any <infl> tag value.
5. Ran rescued_empties_removed_expanded.xml through glottal_conversion.xsl to produce rescued_empties_removed_expanded_fixed.xml. This corrects a bunch of Unicode character representations.
6. Ran rescued_empties_removed_expanded_fixed.xml through collapse_forms_etc.xsl to produce rescued_empties_removed_expanded_fixed_forms_collapsed.xml. This makes a set of changes SK identified as being uniform and helpful to reduce the amount of repetitive work she has to do.
7. Renamed rescued_empties_removed_expanded_fixed_forms_collapsed.xml to rescued_final.xml

Where entries are missing from the other files, SK will now go to rescued_final.xml and retrieve them from there; they should be in the same condition as the other entries they're being merged with.

Note to self: it was difficult to reconstruct this conversion sequence because half of it took place before the blog was in place. In future, make sure anything like this is blogged in great detail.