I believe there may be a bug in applying formatting to runs directly. When directly creating character styles and applying them to a run, the document would not look correct. I added a for loop to manually force the style to be respected to resolve, but this seems problematic. If lines 142 & 143 of the attached are commented out, it fails to apply formatting.

code that shows potential bug
##for github check.txt

output w/out commenting:
annotated-procedure.docx

output w/ commenting:
annotated-procedure.docx

associated input files:
original-procedure.docx
previous-entry.docx