We encountered the same situation with our conversion project. We made the
decision to include information about missing parts of a collection in the
finding itself, including a note at the most appropriate level.

The EAD tag library says that <scopecontent> may be used to describe "gaps"
in a collection, and missing materials certainly are that.

If an entire container (box) is missing, we usually note that information in
a <scopecontent> nested within the main <scopecontent> and include a <head>
that reads "Missing Material."

We also note missing material at the appropriate component level, again
using <scopecontent>.