(e.g. dne~, dns~, ihu~, ihm~, cm~, kl~, etc.do not attempt to represent the abbreviation stroke; instead surround such ordinary letters and entities as the word contains by <ABBR> ... </ABBR> tags:
[for domine, dominus, iesu, iesum, capitulum, kalendas])
<ABBR>dne</ABBR>, <ABBR>ihu</ABBR>
This excludes bits that we are already excluding by means of other tags, especially <FIGURE> and <FOREIGN>.
But it includes individual characters that can be judged from the context to be without definite identity. E.g.,
"The scribe sometimes adds to his 'd's a squiggle that looks a little like this: ~"
Render this as:
"The scribe sometimes adds to his 'd's a squiggle that looks a little like this: <GAP>"
If it is a single character or object, the plain <GAP> will do. If there are more characters than one involved, use lt;GAP EXTENT="3"gt; (or whatever, where "3" is the number of objects involved).